Biomolecular substrate and method and apparatus for examination and diagnosis using the same

ABSTRACT

An object of the present invention is to provide a test apparatus for testing a DNA substrate on which a plurality of DNA fragments for testing are arranged, wherein absolute precision is not required. The above-described problem was solved by providing a substrate on which a plurality of biomolecule spots containing a group of biomolecules (e.g., DNA, etc.) of a specific type are formed, where the pattern or position of the DNA spot is changed depending on specific data so that information of the specific data is recorded on the substrate.

TECHNICAL FIELD

[0001] The present invention relates to a substrate for use in a testfor detecting a biomolecule (e.g., DNA, RNA, a protein, a low-weightorganic molecule (ligand, etc.), sugar, lipid, etc.), a biomoleculechip, and a detection apparatus and test (including screening) anddiagnosis methods using the same.

BACKGROUND ART

[0002] Recently, science and technologies related to genes have beendeveloped more remarkably than expected. As a technique for detecting,analyzing and measuring genetic information, an apparatus called abiomolecule chip (including a DNA chip, a biochip, a microarray, aprotein chip, etc.) and a test method using the same have recentlyreceived attention. A number of different nucleic acids (DNA such ascDNA and genomic DNA, RNA, PNA, etc.) or peptides are arranged and fixedin spotted pattern on a substrate made of glass or silicon. On thissubstrate, fragments of sample DNA to be tested are hybridized with alabeling substance, such as a fluorophore or an isotope or the like, andcapture DNA, or alternatively, a sample polypeptide or ligand to betested is conjugated with a labeling protein by means of theirinteraction. A detector is used to detect fluorescence from the labeledDNA or the labeling peptide in each spot, or a radiation detector isused to detect radioactivity therefrom, thereby obtaining information onarrangement of labeled DNA or labeling peptide spots. By analyzing thisdata, genetic information on the sample DNA can be obtained.

[0003] A gene detection method using a DNA chip or the like has thepotential to be widely used in the analysis of genes for the diagnosisof a disease or analysis of an organism in the future. Examples of achip application include screening of a compound library forcombinatorial chemistry or the like. The versatility of the chips alsohas received attention.

[0004] To date, however, methods for fabricating biomolecule chips asdescribed above require high-precision equipment, leading to high costfor a detection substrate. Moreover, an apparatus for detecting alabeled DNA requires high precision, and therefore, it is difficult forsuch an apparatus to come into widespread use in small business entitiesor practitioners. Biomolecule chips do not have sufficient ability toprocess a large amount of data. Therefore, a substrate or a chip capableof processing data in an easy and efficient manner is expected.

[0005] Problems to be Solved by the Invention

[0006] The above-described detection substrate or detection apparatusdemands a method which does not require high precision. An object of thepresent invention is to provide a system which can be made even using apoor-precision test apparatus and in which system a test can beperformed.

DISCLOSURE OF THE INVENTION

[0007] To solve the above-described problem, the present inventionprovides an apparatus comprising a substrate on which a plurality ofbiomolecule spots made of a specific type of biomolecule (e.g., DNA,etc.), in which a pattern or arrangement of the spot of the biomolecule(e.g., DNA) is changed depending on specific data so that the data isrecorded on the substrate.

[0008] Therefore, the present invention provides the following.

[0009] In one aspect, the present invention provides a method forfabricating a biomolecule substrate, comprising the steps of: 1)providing a set of biomolecules and a substrate; 2) enclosing the set ofbiomolecules into microcapsules on thebiomolecule-type-by-biomolecule-type basis; and 3) spraying thebiomolecule microcapsules onto the substrate.

[0010] In one embodiment, the present invention further comprises thestep of washing the biomolecule microcapsules after the enclosing step.

[0011] In another embodiment, the spraying step is performed by an inkjet method.

[0012] In another embodiment, the ink jet method is performed by aBubble Jet® method.

[0013] In another embodiment, the present invention further comprisesthe step of setting the temperature of a solution used in the sprayingstep to be higher than the melting point of a shell of the biomoleculemicrocapsulate.

[0014] In another embodiment, the microcapsules of the set ofbiomolecules of different types are disposed at different positions.

[0015] In another embodiment, the spraying step is performed by a PINmethod.

[0016] In another embodiment, the biomolecule contains at least one ofDNA, RNA and a peptide.

[0017] In another embodiment, the biomolecule is DNA.

[0018] In another embodiment, the biomolecule is cDNA or genomic DNA.

[0019] In another embodiment, the present invention further comprisesthe step of perform labeling specific to each microcapsule.

[0020] In another aspect, the present invention provides a biomoleculechip, comprising: a substrate; and biomolecules and chip attribute dataarranged on the substrate, wherein the chip attribute data is arrangedin the same region as that of the biomolecules.

[0021] In one embodiment, the chip attribute data contains informationrelating to chip ID and the substrate.

[0022] In another embodiment, the present invention further comprises arecording region, wherein the recording region is placed on the samesubstrate as that of the biomolecule and the chip attribute data, and atleast one of subject data and measurement data is recorded in therecording region.

[0023] In another embodiment, the chip attribute data is recorded insuch a manner as to be read out by the same means as that for detectingthe biomolecule.

[0024] In another embodiment, a specific mark is attached to thesubstrate.

[0025] In another embodiment, a specific mark is arranged based on thechip attribute data.

[0026] In another embodiment, the chip attribute data contains thebiomolecule attribute data.

[0027] In another embodiment, information relating to an address of thebiomolecule is further recorded.

[0028] In another embodiment, the address is a tracking address.

[0029] In another embodiment, the chip attribute data is encrypted.

[0030] In another embodiment, data relating to a label used to detectthe biomolecule is recorded.

[0031] In another embodiment, the data relating to the label contains atleast one of the wavelength of excited light and the wavelength offluorescence.

[0032] In another embodiment, the biomolecule contains at least one ofDNA, RNA and a peptide.

[0033] In another embodiment, the biomolecule is DNA.

[0034] In another embodiment, the biomolecule is cDNA or genomic DNA.

[0035] In another aspect, the present invention provides a biomoleculechip, comprising: 1) a substrate; and 2) biomolecules arranged on thesubstrate, wherein spots of the biomolecules are spaced by at least onenon-equal interval, an address of the biomolecule spot can be identifiedfrom the non-equal interval.

[0036] In one embodiment, the non-equal interval is modulated.

[0037] In another embodiment, the non-equal interval is present in atleast two directions.

[0038] In another aspect, the present invention provides a biomoleculechip. This biomolecule chip comprises: 1) a substrate; and 2)biomolecules arranged on the substrate, wherein the biomolecules includea distinguishable first biomolecule and a distinguishable secondbiomolecule, an address of the biomolecule can be identified based on anarrangement of spots of the first biomolecules and spots of the secondbiomolecule.

[0039] In one embodiment, a label distinguishable from the biomoleculeis placed between the biomolecule spots.

[0040] In another embodiment, the distinguishable label can be detectedby detection means.

[0041] In another embodiment, the label is arranged in a horizontaldirection and a vertical direction on the substrate.

[0042] In another embodiment, a synchronization mark is arranged.

[0043] In another embodiment, the biomolecule contains at least one ofDNA, RNA and a peptide.

[0044] In another embodiment, the biomolecule is DNA.

[0045] In another embodiment, the biomolecule is cDNA or genomic DNA.

[0046] In another aspect, the present invention provides a biomoleculechip, comprising: 1) a substrate; and 2) biomolecules arranged on thesubstrate, wherein spots storing attribute data are arranged on a sideof the substrate opposite to a side on which spots of the biomoleculesare arranged.

[0047] In another embodiment, the attribute data is address information.

[0048] In another aspect, the present invention provides a biomoleculechip, comprising: 1) a substrate; 2) biomolecules arranged on thesubstrate; and 3) a data recording region.

[0049] In one embodiment, the data recording region is placed on theside opposite to the side on which the biomolecules are arranged.

[0050] In another aspect, the present invention provides a method fordetecting a label of a biomolecule chip, comprising the steps of: 1)providing a biomolecule chip on which at least one labeled biomoleculeis arranged; 2) switching detection elements sequentially for detectingthe biomolecules on the biomolecule chip; and 3) identifying a signaldetected by the detection element.

[0051] In one embodiment, the present invention further comprises: 4)adding up each detected signal.

[0052] In another embodiment, the signal is separated by a wavelengthseparation mirror.

[0053] In another embodiment, the biomolecule substrate further containsa synchronization mark, and the label is identified based on thesynchronization mark.

[0054] In another embodiment, the biomolecule substrate contains addressinformation on a rear side of the biomolecule, and the label isidentified based on the address information.

[0055] In another aspect, the present invention provides a method fordetecting information on an organism, comprising the steps of: 1)providing a biomolecule sample from the organism; 2) providing thebiomolecule chip of the present invention; 3) contacting the biomoleculesample to the biomolecule chip, and placing the biomolecule chip underconditions which causes an interaction between the biomolecule sampleand a biomolecule placed on the biomolecule; and 4) detecting a signalcaused by the biomolecule and a signal caused by the interaction,wherein the signal is an indicator for at least one informationparameter of the organism, and the signal is related to an addressassigned to the non-equal interval or the spot arrangement.

[0056] In another embodiment, the biomolecule sample contains nucleicacid, and the biomolecule placed on the biomolecule chip is nucleicacid.

[0057] In another embodiment, the sample contains a protein and thebiomolecule placed on the biomolecule chip is an antibody, or the samplecontains an antibody and the biomolecule placed on the biomolecule chipis a protein.

[0058] In another embodiment, the present invention further compriseslabeling the biomolecule sample with a label molecule.

[0059] In another embodiment, the label molecule can be distinguishedfrom the biomolecule placed on the biomolecule chip.

[0060] In another embodiment, the label molecule contains a fluorescentmolecule, a photophorescent molecule, a chemoluminescent molecule, or aradioactive isotope.

[0061] In another embodiment, the signal detecting step is performed ata site different from where the interaction occurs.

[0062] In another embodiment, the signal detecting step is performed atthe same site as where the interaction occurs.

[0063] In another embodiment, the present invention further comprisesencrypting the signal.

[0064] In another embodiment, the present invention further comprisessubjecting the signal to filtering so as to extract only signal relatingto required information.

[0065] In another aspect, the present invention provides a method fordiagnosing a subject, comprising the steps of: 1) providing a samplefrom the subject; 2) providing the biomolecule chip of the presentinvention; 3) contacting the biomolecule sample to the biomolecule chip,and placing the biomolecule chip under conditions which cause aninteraction between the biomolecule sample and a biomolecule placed onthe biomolecule; 4) detecting a signal caused by the biomolecule and asignal caused by the interaction, wherein the signal is at least onediagnostic indicator for the subject, and the signal is related to anaddress assigned to the non-equal interval or the spot arrangement; and5) determining the diagnostic indicator from the signal.

[0066] In another embodiment, the sample is nucleic acid, and thebiomolecule placed on the biomolecule chip is nucleic acid.

[0067] In another embodiment, the sample contains a protein and thebiomolecule placed on the biomolecule chip is an antibody, or the samplecontains an antibody and the biomolecule placed on the biomolecule chipis a protein.

[0068] In another embodiment, the present invention further compriseslabeling the sample with a label molecule.

[0069] In another embodiment, the label molecule can be distinguishedfrom the biomolecule placed on the biomolecule chip.

[0070] In another embodiment, the label molecule is a fluorescencemolecule, a photophorescent molecule, a chemoluminescent molecule, or aradioactive isotope.

[0071] In another embodiment, the diagnostic indicator is an indicatorfor a disease or a disorder.

[0072] In another embodiment, the diagnostic indicator is based onsingle nucleotide polymorphism (SNP).

[0073] In another embodiment, the diagnostic indicator is based on agenetic disease.

[0074] In another embodiment, the diagnostic indicator is based on theexpression level of a protein.

[0075] In another embodiment, the diagnostic indicator is based on atest result of a biochemical test.

[0076] In another embodiment, the determining step is performed at asite different from where the interaction occurs.

[0077] In another embodiment, the signal detecting step is performed atthe same site as where the interaction occurs.

[0078] In another embodiment, the present invention further comprisesencrypting the signal.

[0079] In another embodiment, the present invention further comprisessubjecting the signal to filtering so as to extract only signal relatingto required information.

[0080] In another embodiment, in the detecting step biomoleculeattribute data is hidden, and in the determining step personalinformation data is hidden.

[0081] In another aspect, the present invention provides a testapparatus for information on an organism, comprising: 1) the biomoleculechip of the present invention; 2) a sample applying section in fluidcommunication with the biomolecule chip; 3) a reaction control sectionfor controlling a contact and an interaction between the biomoleculeplaced on the biomolecule and a biomolecule sample applied from thesample applying section; and 4) a detection section for detecting asignal caused by the interaction, wherein the signal is an indicator forat least one information parameter of the organism, and the signal isrelated to an address assigned to the non-equal interval or the spotarrangement.

[0082] In another embodiment, the present invention further comprises asection for receiving and sending the signal.

[0083] In another embodiment, the present invention further comprises aregion for recording the signal.

[0084] In another aspect, the present invention provides a diagnosisapparatus for a subject. This diagnosis apparatus comprisies: 1) thebiomolecule chip of the present invention; 2) a sample applying sectionin fluid communication with the biomolecule chip; 3) a reaction controlsection for controlling a contact and an interaction between thebiomolecule placed on the biomolecule and a biomolecule sample appliedfrom the sample applying section; 4) a detection section for detecting asignal caused by the biomolecule and a signal caused by the interaction,wherein the signal is an indicator for at least one informationparameter of the organism, and the signal is related to an addressassigned to the non-equal interval or the spot arrangement; and 5)determining the diagnostic indicator from the signal.

[0085] In one embodiment, the present invention further comprises asection for receiving and sending the signal.

[0086] In another embodiment, the present invention further comprises aregion for recording the signal.

[0087] In one aspect, the present invention provides a biological testsystem. This biological test system comprises: A) a main sub system,comprising: 1) the biomolecule chip of the present invention; 2) asample applying section in fluid communication with the biomoleculechip; 3) a reaction control section for controlling a contact and aninteraction between the biomolecule placed on the biomolecule and abiomolecule sample applied from the sample applying section; 4) adetection section for detecting a signal caused by the biomolecule and asignal caused by the interaction, wherein the signal is an indicator forat least one information parameter of the organism, and the signal isrelated to an address assigned to the non-equal interval or the spotarrangement; and 5) a sending and receiving section for sending andreceiving a signal, and B) a sub sub system, comprising: 1) a sendingand receiving section for sending and receiving a signal; and 2) a testsection for calculating a test value from the signal received from themain sub system. The main sub system and the sub sub system areconnected together via a network.

[0088] In another embodiment, the signal received by the sub sub systemcontains a signal relating to measurement data measured by the sub subsystem.

[0089] In another embodiment, the attribute data contains chip ID,personal information data, and biomolecule attribute data, the main subsystem contains the chip ID and the personal information data, but doesnot contain the biomolecule attribute data, and the sub sub systemcontains the chip ID and the biomolecule attribute data, but does notcontain the personal information data, and the sub sub system sends thetest value, determined in response to a request, to the main sub system.

[0090] In another embodiment, the network is the Internet.

[0091] In another embodiment, the signal to be sent and received isencrypted.

[0092] In another aspect, the present invention provides a diagnosissystem. This diagnosis system comprises: A) a main sub system,comprising: 1) the biomolecule chip of the present invention; 2) asample applying section in fluid communication with the biomoleculechip; 3) a reaction control section for controlling a contact and aninteraction between the biomolecule placed on the biomolecule and abiomolecule sample applied from the sample applying section; 4) adetection section for detecting a signal caused by the biomolecule and asignal caused by the interaction, wherein the signal is an indicator forat least one information parameter of the organism, and the signal isrelated to an address assigned to the non-equal interval or the spotarrangement; and 5) a sending and receiving section for sending andreceiving a signal, and B) a sub sub system, comprising: 1) a sendingand receiving section for sending and receiving a signal; and 2) adetermination section for determining the diagnostic indicator from thesignal received from the main sub system. The main sub system and thesub sub system are connected together via a network.

[0093] In another embodiment, the signal received by the sub sub systemcontains a signal relating to measurement data measured by the sub subsystem.

[0094] In another embodiment, the attribute data contains chip ID,personal information data, and biomolecule attribute data, the main subsystem contains the chip ID and the personal information data, but doesnot contain the biomolecule attribute data, and the sub sub systemcontains the chip ID and the biomolecule attribute data, and data fordetermining a diagnostic indicator from biomolecule attribute data, butdoes not contain the personal information data, and the sub sub systemsends the diagnostic indicator, determined in response to a request, tothe main sub system.

[0095] In another embodiment, the network is the Internet.

[0096] In another embodiment, the signal to be sent and received isencrypted.

[0097] In another embodiment, the present invention provides a testapparatus for biological information. This test apparatus comprises: asupport for a substrate; a plurality of groups of biomolecules arrangedon the substrate, each group containining the biomolecules of the sametype; shifting means for shifting the substrate; a light source forexciting a fluorescence substance labeling a sample to be tested; andoptical means for converging light from the light source. The lightsource is caused to emit light intermittently in response to anintermittent emission signal so as to excite the fluorescence substance,fluorescence from the fluorescence substance is detected by aphotodetector during a period of time when the intermittent emissionsignal is paused, identification information is reproduced from anarrangement of the DNAs, and the biomolecules emitting fluorescence isidentified.

[0098] In another embodiment, the present invention further comprisesmeans for adding up detected detection signals.

[0099] In another embodiment, the present invention further comprises awavelength separation mirror.

[0100] In another embodiment, the present invention provides use of thebiomolecule chip of the present invention for fabricating an apparatusfor testing biological information.

[0101] In another embodiment, the present invention provides use of thebiomolecule chip of the present invention for fabricating an apparatusfor diagnosing a subject.

BRIEF DESCRIPTION OF THE DRAWINGS

[0102] The present invention will be herein described with reference tothe drawings briefly described below. The drawings are provided for thepurpose of illustrating preferable embodiments of the present invention,but not for the purpose of restricting the scope of the presentinvention. The scope of the present invention is specified only by theclaims attached thereto. Each figure will be described below.

[0103]FIG. 1:

[0104] (a) A top view showing a substrate on which DNA is placed,according to an embodiment of the present invention.

[0105] (b) A cross-sectional view showing a substrate on which DNA isplaced, according to an embodiment of the present invention.

[0106]FIG. 2:

[0107] A diagram showing a method for fabricating a DNA microcapsuleaccording to an embodiment of the present invention.

[0108]FIG. 3:

[0109] A diagram shown in a method for attaching DNA by a pin methodaccording to an embodiment of the present invention.

[0110]FIG. 4:

[0111] A diagram showing a method for shifting DNA to a pin according toan embodiment of the present invention.

[0112]FIG. 5:

[0113] A top view showing a DNA chip according to an embodiment of thepresent invention, and a data structure diagram.

[0114]FIG. 6:

[0115] A diagram showing a structure of DNA substrate attribute dataaccording to an embodiment of the present invention.

[0116]FIG. 7:

[0117] A diagram showing a method for fixing DNA according to anembodiment of the present invention.

[0118]FIG. 8:

[0119] A schematic diagram showing a method for fixing DNA according toan embodiment of the present invention.

[0120]FIG. 9:

[0121] A block diagram showing a method for ejecting DNA by an ink jetmethod according to an embodiment of the present invention.

[0122]FIG. 10:

[0123] A diagram showing an arrangement of DNA on a substrate accordingto an embodiment of the present invention.

[0124]FIG. 11:

[0125] A diagram showing ejection in an ink jet method according to anembodiment of the present invention.

[0126]FIG. 12:

[0127] A diagram showing an arrangement of DNA spots on a substrateaccording to an embodiment of the present invention.

[0128]FIG. 13:

[0129] A diagram showing hybridization of labeled DNA according to anembodiment of the present invention.

[0130]FIG. 14:

[0131] A block diagram showing a test apparatus according to anembodiment of the present invention.

[0132]FIG. 15:

[0133] A flowchart showing ejection of a microcapsule according to anembodiment of the present invention.

[0134]FIG. 16:

[0135] A diagram showing an operation of a mirror according to anembodiment of the present invention.

[0136]FIG. 17:

[0137] A diagram showing a relationship between excited light andfluorescence according to an embodiment of the present invention.

[0138]FIG. 18:

[0139] A diagram showing scanning of DNA spots according to anembodiment of the present invention.

[0140]FIG. 19:

[0141] A diagram showing a relationship between a light receiving arrayand fluorescence according to an embodiment of the present invention.

[0142]FIG. 20:

[0143] A timing chart showing detection of fluorescence according to anembodiment of the present invention.

[0144]FIG. 21:

[0145] A block diagram showing a photodetector comprising a lightreceiving array according to an embodiment of the present invention.

[0146]FIG. 22:

[0147] A diagram showing exemplary data of a label detection signalaccording to an embodiment of the present invention.

[0148]FIG. 23:

[0149] A diagram showing a principle of a detection apparatus accordingto an embodiment of the present invention.

[0150]FIG. 24:

[0151] A diagram showing a principle of a detection apparatus accordingto an embodiment of the present invention.

[0152]FIG. 25:

[0153] A top view showing a relationship between a DNA spot and a trackaccording to an embodiment of the present invention.

[0154]FIG. 26:

[0155] A diagram showing an arrangement of DNA spots according to anembodiment of the present invention.

[0156]FIG. 27:

[0157] A top view showing a circular substrate according to anembodiment of the present invention.

[0158]FIG. 28:

[0159] A diagram showing a DNA area of a circular substrate according toan embodiment of the present invention.

[0160]FIG. 29:

[0161] A diagram showing a procedure for fabricating a DNA substrateusing a semiconductor process method according to an embodiment of thepresent invention.

[0162]FIG. 30:

[0163] A diagram showing a principle of an ink jet method according toan embodiment of the present invention.

[0164]FIG. 31:

[0165] A flowchart showing a method for detecting fluorescence byscanning a plurality of times according to an embodiment of the presentinvention.

[0166]FIG. 32:

[0167] A timing chart showing excited light and detected light in amethod for scanning a plurality of times according to an embodiment ofthe present invention.

[0168]FIG. 33:

[0169] A diagram showing a method for fabricating a biomolecule chip bya tube method according to an embodiment of the present invention.

[0170]FIG. 34:

[0171] A diagram showing another method for fabricating a biomoleculechip by a tube method according to an embodiment of the presentinvention.

[0172]FIG. 35:

[0173] A diagram showing an arrangement of biomolecule spots by a tubemethod according to an embodiment of the present invention and a diagramshowing buried data.

[0174]FIG. 36:

[0175] A diagram showing an arrangement of biomolecule spots by a tubemethod according to an embodiment of the present invention and a diagramshowing buried data.

[0176]FIG. 37:

[0177] A diagram showing an arrangement of biomolecule spots by a tubemethod according to an embodiment of the present invention.

[0178]FIG. 38:

[0179] A diagram showing a method for arranging a biomolecule spot by apin method according to an embodiment of the present invention.

[0180]FIG. 39:

[0181] A diagram showing a method for arranging a biomolecule spot by anink jet method according to an embodiment of the present invention.

[0182]FIG. 40:

[0183] A diagram showing a table of an identification number and abiomolecule attribute data according to an embodiment of the presentinvention.

[0184]FIG. 41:

[0185] A flowchart showing a detection procedure using a pin methodaccording to an embodiment of the present invention.

[0186]FIG. 42:

[0187] A diagram showing a data structure of data containing ECC buriedby a tube method according to an embodiment of the present invention.

[0188]FIG. 43:

[0189] A block diagram showing a network type test system according toan embodiment of the present invention.

[0190]FIG. 44:

[0191] A block diagram showing a stand-alone type test system accordingto an embodiment of the present invention.

[0192]FIG. 45:

[0193] A diagram showing a table of analysis results according to anembodiment of the present invention.

[0194]FIG. 46:

[0195] A diagram showing a structure of a biomolecule chip according toan embodiment of the present invention.

[0196]FIG. 47:

[0197] A diagram showing a structure according to an embodiment of thepresent invention, in which an address can be specified by a specificarrangement.

[0198]FIG. 48:

[0199] A diagram showing a structure of a biomolecule chip according toan embodiment of the present invention, in which an address can bespecified by a specific pattern.

DESCRIPTION OF REFERENCE NUMERALS

[0200]1 substrate

[0201]2 DNA spot

[0202]3 DNA

[0203]4 main solution

[0204]5 main film

[0205]6 DNA microcapsule

[0206]7 sub-film

[0207]8 sub-solution

[0208]9 microcapsule

[0209]10 main container

[0210]11 container

[0211]12 tray

[0212]13 pin

[0213]14 moving pin

[0214]15 washing section

[0215]16 pin drum

[0216]17 DNA spot region

[0217]18 data region

[0218]19 substrate ID

[0219]20 DNA number-position correspondence table

[0220]21 DNA sequence data

[0221]22 labeled DNA

[0222]23 empty microcapsule

[0223]24 nozzle

[0224]25 supply section

[0225]26 eject section (heater)

[0226]27 eject control circuit

[0227]28 master control section

[0228]29 eject signal generation section

[0229]30 removal signal generation section

[0230]31 photodetector

[0231]32 unnecessary liquid removing section

[0232]33 deviation section

[0233]34 arrow

[0234]35 shift amount detector

[0235]36 shift control circuit

[0236]37 synchronization mark

[0237]38 fluorescence dye

[0238]39 detection apparatus

[0239]40 light source (for excitation)

[0240]41 mirror

[0241]42 lens

[0242]43 detection section

[0243]44 focus error signal detection section

[0244]45 tracking error signal detection section

[0245]46 focus control circuit

[0246]47 tracking control circuit

[0247]48 actuator

[0248]49 focus offset signal generation section

[0249]50 track offset signal generation section

[0250]51 spot number output section

[0251]52 track number output section

[0252]53 ECC decoder

[0253]54 DNA substrate attribute data reading portion

[0254]55 data processing section

[0255]56 synchronization signal generation section

[0256]57 substrate shift section

[0257]58 capture DNA number

[0258]59 second label signal detection section

[0259]60 first label signal detection section

[0260]61 first label signal output section

[0261]62 second label signal output section

[0262]63 data output section

[0263]64 positional information detection section

[0264]65 mirror

[0265]66 mirror

[0266]67 label signal detection section

[0267]68 step

[0268]69 main signal reproduction section

[0269]70 detection cell

[0270]71 excitation beam

[0271]72 scanning track

[0272]73 encryption key

[0273]74 cipher decoder

[0274]75 factory-shipped data region

[0275]76 postscript data region

[0276]77 first label attribute data

[0277]78 second label attribute data

[0278]79 synchronization data

[0279]80 data reproduction area

[0280]85 label detection signal

[0281]86 shift amount detector

[0282]87 pulsed light emission control section

[0283]88 pulsed light emission signal

[0284]89 sub-pulsed light emission signal

[0285]90 light detection section

[0286]91 array

[0287]92 switching section

[0288]93 addition section

[0289]94 label detection signal list

[0290]95 recording layer

[0291]96 address

[0292]97 start address

[0293]98 end address

[0294]99 innermost circumferential track number

[0295]100 outermost circumferential track number

[0296]111 counter

[0297]112 address counter

[0298]113 address block counter

[0299]114 sub-eject section

[0300]115 sub-solution supply section

[0301]116 sub-nozzle

[0302]118 step

[0303]120 mask

[0304]121 mask (for DNA spots)

[0305]122 hydroxy group

[0306]123 A (adenine)

[0307]124 C (cytosine)

[0308]125 G (guanine)

[0309]126 T (thymine)

[0310]130 tube

[0311]131 probe

[0312]132 container

[0313]133 sheet

[0314]134 mark tube

[0315]135 solution

[0316]136 mark tube

[0317]137 block

[0318]138 chip

[0319]139 fix plate

[0320]140 fix plate ID

[0321]141 biomolecule spot

[0322]142 mark spot

[0323]143 identification mark

[0324]144 synchronization mark

[0325]145 identification number

[0326]146 attribute table

[0327]147 test database

[0328]148 step (flowchart)

[0329]149 test apparatus

[0330]150 network

[0331]151 memory

[0332]152 error correction code

[0333]153 mark solution

[0334]154 mark biomolecule spot

[0335]155 analysis program

[0336]156 mark microcapsule

[0337]157 synchronization mark

[0338]158 synchronization mark

[0339]159 original data

[0340]160 flat tube

[0341]161 rectangular biomolecule spot

[0342]162 synchronization mark

[0343]170 subject

[0344]171 sample

[0345]172 biomolecule extraction section

[0346]173 specimen

[0347]174 main test system

[0348]175 test section

[0349]176 communication section

[0350]177 the Internet

[0351]178 sub-test system

[0352]179 communication section

[0353]180 analysis system

[0354]181 analysis section

[0355]182 selection section

[0356]183 output section

[0357]184 (biomolecule spot identification number) attribute database

[0358]185 selective output

[0359]186 request output

[0360]187 diagnosis system

[0361]188 diagnosis section

[0362]189 treatment policy production section

[0363]190 treatment policy output section

[0364]191 chip ID-subject correspondence database

[0365]192 diagnosis result output section

[0366]193 test system

[0367]194 black box section

[0368]195 input/output section

[0369]197 cipher decoding section

[0370]198 IC chip

[0371]199 electrode

[0372]200 substrate

[0373]201 non-volatile memory

[0374]300 biomolecule chip

[0375]301 biomolecule spot

[0376]302 equal interval

[0377]303 non-equal interval

[0378]310 biomolecule chip

[0379]311 first biomolecule spot

[0380]312 second biomolecule spot

BEST MODE FOR CARRYING OUT THE INVENTION

[0381] It should be understood throughout the present specification thatarticles for singular forms (e.g., “a”, “an”, “the”, etc. in English;“ein”, “der”, “das”, “die”, etc. and their inflections in German; “un”,“une”, “le”, “la”, etc. in French; “un”, “una”, “el”, “la”, etc. inSpanish; and articles, adjectives, etc. in other languages) include theconcept of their plurality unless otherwise mentioned. It should be alsounderstood that terms as used herein have definitions ordinarily used inthe art unless otherwise mentioned.

[0382] Hereinafter, the meanings of terms as particularly used hereinwill be described.

[0383] The terms “substrate” and “support” as used herein have the samemeaning, i.e., a material for an array construction of the presentinvention (preferably, in a solid form). Examples of a material for thesubstrate include any solid material having a property of binding to abiomolecule used in the present invention either by covalent bond ornoncovalent bond, or which can be derived in such a manner as to havesuch a property.

[0384] Such a material for the substrate may be any material capable offorming a solid surface, for example, including, but being not limitedto, glass, silica, silicon, ceramics, silica dioxide, plastics, metals(including alloys), naturally-occurring and synthetic polymer (e.g.,polystyrene, cellulose, chitosan, dextran, and nylon). The substrate maybe formed of a plurality of layers made of different materials. Forexample, an inorganic insulating material, such as glass, silica glass,alumina, sapphire, forsterite, silicon carbide, silicon oxide, siliconnitride, or the like, can be used. Moreover, an organic material, suchas polyethylene, ethylene, polypropylene, polyisobutylene, polyethyleneterephthalate, unsaturated polyester, fluorine-containing resin,polyvinyl chloride, polyvinylidene chloride, polyvinyl acetate,polyvinyl alcohol, polyvinyl acetal, acrylic resin, polyacrylonitrile,polystyrene, acetal resin, polycarbonate, polyamide, phenol resin, urearesin, epoxy resin, melamine resin, styrene acrylonitrile copolymer,acrylonitrilebutadienestyrene copolymer, silicone resin, polyphenyleneoxide, or polysulfone, can be used. In the present invention, a filmused for nucleic acid blotting, such as a nitrocellulose film, a PVDFfilm, or the like, can also be used.

[0385] In one embodiment of the present invention, an electrode materialcan be used for a substrate electrode which serves as both a substrateand an electrode. In the case of such a substrate electrode, a surfaceof the substrate electrode is separated into electrode regions by aninsulating layer region. Preferably, different biomolecules are fixed tothe respective isolated electrode regions. The electrode material is notparticularly limited. Examples of the electrode material include a metalalone, such as gold, gold alloy, silver, platinum, mercury, nickel,palladium, silicon, germanium, gallium, tungsten, and the like, andalloys thereof, or carbon, such as graphite, glassy carbon, and thelike, or oxides or compounds thereof. Further, a semiconductor compound,such as silicon oxide and the like, or various semiconductor devices,such as CCD, FET, CMOS, and the like, can be used. When a substrateelectrode in which an electrode film is formed on an insulatingsubstrate so that the substrate is integrated with the electrode, theelectrode film can be produced by plating, printing, sputtering,deposition or the like. In the case of deposition, an electrode film canbe formed by a resistance heating method, a high-frequency heatingmethod, an electron-beam heating method, or the like. In the case ofsputtering, an electrode film can be produced by direct currentsputtering, bias sputtering, asymmetric AC sputtering, gettersputtering, high-frequency sputtering, or the like. Furthermore,electropolymerized film, such as polypyrrole, polyaniline, and the like,or a conductive polymer can be used. An insulating material used forseparating the electrode surface in the present invention is notparticularly limited, but is preferably a photopolymer or a photoresistmaterial. Examples of the resist material include a photoresist forlight exposure, a photoresist for ultraviolet radiation, a photoresistfor X ray, and a photoresist for electron beam. Examples of aphotoresist for light exposure include photoresists including cyclizedrubber, polycinnamic acid, and novolac resin as major ingredients. As aphotoresist for ultraviolet radiation, cyclized rubber, phenol resin,polymethylisopropenylketone (PMIPK), polymethylmethacrylate (PMMA), orthe like is used. As a photoresist for X ray, COP, methacrylate, or thelike can be used. As a photoresist for electron beam, theabove-described substances, such as PMMA or the like, can be used.

[0386] “Chip” as used herein refers to an ultramicro-integrated circuithaving various functions, which constitutes a part of a system.“Biomolecule chip” as used herein refers to a chip comprising asubstrate and a biomolecule, in which at least one biomolecule as setforth herein is disposed on the substrate.

[0387] The term “address” as used herein refers to a unique position ona substrate which can be distinguished from other unique positions. Anaddress is suitably used to access to a biomolecule associated with theaddress. Any entity present at each address can have an arbitrary shapewhich allows the entity to be distinguished from entities present atother addresses (e.g., in an optical manner). The shape of an addressmay be, for example, a circle, an ellipse, a square, or a rectangle, oralternatively an irregular shape.

[0388] The size of each address varies depending on, particularly, thesize of a substrate, the number of addresses on the specific substrate,the amount of samples to be analyzed and/or an available reagent, thesize of a biomolecule, and the magnitude of a resolution required forany method in which the array is used. The size of an address may rangefrom 1-2 nm to several centimeters (e.g., 1-2 mm to several centimeters,etc., 125×80 mm, 10×10 mm, etc.). Any size of an address is possible aslong as it matches the array to which it is applied. In such a case, asubstrate material is formed into a size and a shape suitable for aspecific production process and application of an array. For example, inthe case of analysis where a large amount of samples to be measured areavailable, an array may be more economically constructed on a relativelylarge substrate (e.g., 1 cm×1 cm or more). Here, a detection systemwhich does not require sensitivity much and is therefore economical maybe further advantageously used. On the other hand, when the amount of anavailable sample to be analyzed and/or reagent is limited, an array maybe designed so that consumption of the sample and reagent is minimized.

[0389] The spatial arrangement and forms of addresses are designed insuch a manner as to match a specific application in which the microarrayis used. Addresses may be densely loaded, widely distributed, or dividedinto subgroups in a pattern suitable for a specific type of sample to beanalyzed. “Array” as used herein refers to a pattern of solid substancesfixed on a solid phase surface or a film, or a group of molecules havingsuch a pattern. Typically, an array comprises biomolecules (e.g., DNA,RNA, protein-RNA fusion molecules, proteins, low-weight organicmolecules, etc.) conjugated to nucleic acid sequences fixed on a solidphase surface or a film as if the biomolecule captured the nucleicsequence. “Spots” of biomolecules may be arranged on an array. “Spot” asused herein refers to a predetermined set of biomolecules.

[0390] Any number of addresses may be arranged on a substrate, typicallyup to 10⁸ addresses, in other embodiments up to 10⁷ addresses, up to 10⁶addresses, up to 10⁵ addresses, up to 10⁴ addresses, up to 10³addresses, or up to 10² addresses. Therefore, when one biomolecule isplaced on one address, up to 10⁸ biomolecules can be placed on asubstrate, and in other embodiment up to 10⁷ biomolecules, up to 10⁶biomolecules, up to 10⁵ biomolecules, up to 10⁴ biomolecules, up to 10³biomolecules, or up to 10² biomolecules can be placed on a substrate. Inthese cases, a smaller size of substrate and a smaller size of addressare suitable. In particular, the size of an address may be as small asthe size of a single biomolecule (i.e., this size may be of the order of1-2 nm). In some cases, the minimum area of a substrate is determinedbased on the number of addresses on the substrate.

[0391] The term “biomolecule” as used herein refers to a moleculerelated to an organism. An “organism” as used herein refers to abiological organic body, including, but being limited to, an animal, aplant, a fungus, a virus, and the like. A biomolecule includes amolecule extracted from an organism, but is not so limited. Abiomolecule is any molecule capable of having an influence on anorganism. Therefore, a biomolecule also includes a molecule synthesizedby combinatorial chemistry, and a low weight molecule capable of beingused as a medicament (e.g., a low molecular weight ligand, etc.) as longas they are intended to have an influence on an organism. Examples ofsuch a biomolecule include, but are not limited to, proteins,polypeptides, oligopeptides, peptides, polynucleotides,oligonucleotides, nucleotides, nucleic acids (e.g., including DNA (suchas cDNA and genomic DNA) and RNA (such as mRNA)), polysaccharides,oligosaccharides, lipids, low weight molecules (e.g., hormones, ligands,signal transduction substances, low-weight organic molecules, etc.), andcomplex molecules thereof, and the like. A biomolecule also includes acell itself, and a part or the whole of tissue, and the like as long asthey can be coupled to a substrate of the present invention. Preferably,a biomolecule includes a nucleic acid or a protein. In a preferableembodiment, a biomolecule is a nucleic acid (e.g., genomic DNA or cDNA,or DNA synthesized by PCR or the like). In another preferableembodiment, a biomolecule may be a protein. Preferably, one type ofbiomolecule may be provided for each address on a substrate of thepresent invention. In another embodiment, a sample containing two ormore types of biomolecules may be provided for each address.

[0392] The term “protein”, “polypeptide”, “oligopeptide” and “peptide”as used herein have the same meaning and refer to an amino acid polymerhaving any length. This polymer may be a straight, branched or cyclicchain. An amino acid may be a naturally-occurring ornon-naturally-occurring amino acid, or a variant amino acid. The termmay be assembled into a complex of a plurality of polypeptide chains.The term also includes a naturally-occurring or artificially modifiedamino acid polymer. Such modification includes, for example, disulfidebond formation, glycosylation, lipidation, acetylation, phosphorylation,or any other manipulation or modification (e.g., conjugation with alabeling component). This definition encompasses a polypeptidecontaining at least one amino acid analog (e.g., non-naturally-occurringamino acid, etc.), a peptide-like compound (e.g., peptoid), and othervariants known in the art, for example.

[0393] The terms “polynucleotide”, “oligonucleotide”, and “nucleic acid”as used herein have the same meaning and refer to a nucleotide polymerhaving any length. This term also includes an “oligonucleotidederivative” or a “polynucleotide derivative”. An “oligonucleotidederivative” or a “polynucleotide derivative” includes a nucleotidederivative, or refers to an oligonucleotide or a polynucleotide havingdifferent linkages between nucleotides from typical linkages, which areinterchangeably used. Examples of such an oligonucleotide specificallyinclude 2′-O-methyl-ribonucleotide, an oligonucleotide derivative inwhich a phosphodiester bond in an oligonucleotide is converted to aphosphorothioate bond, an oligonucleotide derivative in which aphosphodiester bond in an oligonucleotide is converted to a N3′-P5′phosphoroamidate bond, an oligonucleotide derivative in which a riboseand a phosphodiester bond in an oligonucleotide are converted to apeptide-nucleic acid bond, an oligonucleotide derivative in which uracilin an oligonucleotide is substituted with C-5 propynyl uracil, anoligonucleotide derivative in which uracil in an oligonucleotide issubstituted with C-5 thiazole uracil, an oligonucleotide derivative inwhich cytosine in an oligonucleotide is substituted with C-5 propynylcytosine, an oligonucleotide derivative in which cytosine in anoligonucleotide is substituted with phenoxazine-modified cytosine, anoligonucleotide derivative in which ribose in DNA is substituted with2′-O-propyl ribose, and an oligonucleotide derivative in which ribose inan oligonucleotide is substituted with 2′-methoxyethoxy ribose.

[0394] “Gene” as used herein refers to a factor defining a genetictrait. A gene is typically arranged in a certain sequence on achromosome. A gene which defines the first-order structure of a proteinis called a structural gene. A gene which regulates the expression of astructural gene is called a regulatory gene. A “gene” as used herein mayrefer to a “polynucleotide”, an “oligonucleotide” and a “nucleic acid”,and/or a “protein”, a “polypeptide”, an “oligopeptide” and a “peptide”.As used herein, “homology” of a gene refers to the magnitude of identitybetween two or more gene sequences. Therefore, the greater the homologybetween two certain genes, the greater the identity or similaritybetween their sequences. Whether or not two genes have homology isdetermined by comparing their sequences directly or by a hybridizationmethod under stringent conditions. When two gene sequences are directlycompared with each other, the genes have representatively at least 50%homology, preferably at least 70% homology, more preferably at least80%, 90%, 95%, 96%, 97%, 98%, or 99% homology with the DNA sequence ofthe genes are identical.

[0395] The term “polysaccharide”, “complex carbohydrate”,“oligosaccharide”, “sugar”, and “carbohydrate” have the same meaning andrefer to a polymer compound in which monosaccharides aredehydrocondensed by glycoside bonds. “Simple sugar” or “monosaccharide”refers to a substance represented by the general formulaC_(n)H_(2n)O_(n), which cannot be decomposed by hydrolysis to a simplermolecule. CnH_(2n)O_(n) where n=2, 3, 4, 5, 6, 7, 8, 9 and 10, representdiose, triose, tetrose, pentose, hexose, heptose, octose, nonose, anddecose, respectively. Monosaccharide generally corresponds to analdehyde or ketone of chain polyhydric alcohol, the former being calledaldose and the latter being called ketose.

[0396] A biomolecule of the present invention may be collected from anorganism or may be chemically synthesized by a method known to thoseskilled in the art. For example, a synthesis method using an automatedsolid phase peptide synthesizer is described in the following: Stewart,J. M. et al. (1984). Solid Phase Peptide Synthesis, Pierce Chemical Co.;Grant, G. A. (1992). Synthetic Peptides: AUser's Guide, W. H. Freeman;Bodanszky, M. (1993). Principles of Peptide Synthesis, Springer-Verlag;Bodanszky, M. et al. (1994). The Practice of Peptide Synthesis,Springer-Verlag; Fields, G. B. (1997). Phase Peptide Synthesis, AcademicPress; Pennington, M. W. et al. (1994). Peptide Synthesis Protocols,Humana Press; Fields, G. B. (1997). Solid-Phase Peptide Synthesis,Academic Press. An oligonucleotide may be prepared by automated chemicalsynthesis using any DNA synthesizer commercially available from AppliedBiosystems or the like. A composition and a method for automatedoligonucleotide synthesis are disclosed in, for example, U.S. Pat. No.4,415,732, Caruthers et al. (1983); U.S. Pat. No. 4,500,707,Caruthers(1985); and U.S. Pat. No. 4,668,777, Caruthers et al. (1987).

[0397] In one embodiment of the present invention, a library ofbiomolecules (e.g., low-weight organic molecules, combinatorialchemistry products) may be coupled to a substrate, and a resultantsubstrate can be used to produce a microarray for screening ofmolecules. A compound library used in the present invention can beprepared or obtained by any means including, but not limited to, acombinatorial chemistry technique, a fermentation method, extractionprocedures from plants and cells, or the like. A method for producing acombinatorial library is well known in the art. See, for example, E. R.Felder, Chimia 1994, 48, 512-541; Gallop et al., J. Med. Chem. 1994, 37,1233-1251; R. A. Houghten, Trends Genet. 1993, 9, 235-239; Houghten etal., Nature 1991, 354, 84-86; Lam et al., Nature 1991, 354, 82-84;Carell et al., Chem. Biol. 1995, 3, 171-183; Madden et al., Perspectivesin Drug Discovery and Design2, 269-282; Cwirla et al., Biochemistry1990, 87, 6378-6382; Brenner et al., Proc. Natl. Acad. Sci. USA 1992,89, 5381-5383; Gordon et al., J. Med. Chem. 1994, 37, 1385-1401; Lebl etal., Biopolymers 1995, 37 177-198; and literature cited therein. Thesepublications are herein incorporated by reference in their entirety.

[0398] “Stringent conditions” as used herein refers to widely used andwell known conditions in the art concerning hybridization. Suchconditions are, for example, the following: hybridization is conductedin the presence of 0.7 to 1.0 M NaCl at 65° C., and thereafter, 0.1 to2-fold concentration SSC (saline-sodium citrate) solution (1-foldconcentration SSC solution has a composition of 150 mM sodium Chloride,15 mM sodium citrate) is used to wash a filter at 65° C. Hybridizationcan be conducted in accordance with a method described in anexperimental manual, such as Molecular Cloning 2nd ed., CurrentProtocols in Molecular Biology, Supplement 1-38, DNA Cloning 1: CoreTechniques, A Practical Approach, Second Edition, Oxford UniversityPress (1995), or the like.

[0399] Comparison in identity between base sequences is hereincalculated by a sequence analyzing tool, BLAST, using defaultparameters.

[0400] A method, biomolecule chip and apparatus of the present inventionmay be used in, for example, diagnosis, forensic medicine, drug search(medicament screening) and development, molecular biological analysis(e.g., array-base nucleotide sequence analysis and array-base genesequence analysis), analysis of protein properties and functions,pharmacogenomics, proteomics, environmental assessment, and otherbiological and chemical analysis.

[0401] A method, biomolecule chip and apparatus of the present inventionmay be used in the detection of various genes. A gene to be detected isnot particularly limited. Examples of such a gene to be detected includegenes of viral pathogens (including, but not limited to, hepatitisviruses (type A, B, C, D, E, F, and G), HIV, influenza viruses, herpesviruses, adenovirus, human polyoma virus, human Papilloma virus, humanParvovirus, mumps virus, human rotavirus, Enterovirus, Japaneseencephalitis virus, dengue virus, rubella virus, and HTLV); genes ofbacterial pathogens (including, but not limited to, Staphylococcusaurens, hemolytic streptococcus, virulent Escherichia coli, enteritisvibrio, Helicobacter pylori, Campylobacter, Vibrio cholerae, dysenterybacillus, Salmonella, Yersinia, gunococcus, Listeria monocytogenes,Leptospira, Legionella, Spirochaeta, Mycoplasma pneumoniae, Rickettsia,and Chlamydia), and genes of Entamoeba histolytica, pathogenic fungi,parasites, and fungi.

[0402] A method, biomolecule chip and apparatus of the present inventionmay be used in detection and diagnosis for neoplastic diseases, such ashereditary diseases, retinoblastoma, Wilms' tumor, familial colonicpolyposis, neurofibromatosis, familial breast cancer, xerodermapigmentosum, brain tumor, cancer of the oral cavity, esophageal cancer,stomach cancer, colon cancer, liver cancer, pancreas cancer, lungcancer, thyroid tumor, tumor of the mammary gland, tumor of urinaryorgans, tumor of male organs, tumor of female organs, skin tumor, tumorof bones and soft parts, leukemia, lymphoma, solid tumor, and the like.

[0403] The present invention can also be applied to polymorphismanalysis, such as RFLP analysis, SNP (snipp, single nucleotidepolymorphism) analysis, or the like, analysis of base sequences, and thelike. The present invention can also be used for screening of amedicament.

[0404] The present invention can be applied to any situation requiring abiomolecule test other than medical applications, such as food testing,quarantine, medicament testing, forensic medicine, agriculture,husbandry, fishery, forestry, and the like. The present invention isalso intended to be used particularly for the purposes of safety offoods (BSE test).

[0405] The present invention may be used to obtain biochemical testdata. Examples of items of biochemical tests include, but are notlimited to, total protein, albumin, thymol reaction, Kunkel's zincsulfate testing, plasma ammonia, urea nitrogen, creatinine, uric acid,total bilirubin, direct reacting bilirubin, GOT, GPT, cholinesterase,alkaline phosphatase, leucine aminopeptidase, γ-glutamyl transpeptidase,creatinine phosphakinase, lactic dehydrogenase, amylase, sodium,potassium, chloride ion (chlor), total calcium, inorganic phosphor,serum iron, unsaturated iron-binding capability, serum osmotic pressure,total cholesterol, free cholesterol, HDL-cholesterol, triglyceride,phospholipid, free fatty acid, plasma glucose, insulin, BSP retentionratio, ICG disappearance ratio, ICG retention ratio, spinal fluid•totalprotein, spinal•fluid sugar, spinal fluid•chlorine, urine·total protein,urine•glucose, urine•amylase, urine•ureic acid, urine•urea nitrogen,urine•creatinine, urine•calcium, urine•osmotic pressure, urine•inorganicphosphor, urine·sodium, urine•potassium, urine•chlor,N-acetylglucosamimidase in urine, 1-hour creatinine clearance, 24-hourcreatinine clearance, phenolsulfonephthalein, C-reactive protein, andthe like. A method and principle for measuring these test items are wellknown and commonly used in the art.

[0406] The present invention can also be used for detection of a geneamplified by PCR, SDA, NASBA, or the like, other than a sample directlycollected from an organism. In the present invention, a target gene canbe labeled in advance with an electrochemically active substance, afluorescent substance (e.g., FITC, rhodamine, acridine, Texas Red,fluorecein, etc.), an enzyme (e.g., alkaline phosphatase, peroxidase,glucose oxidase, etc.), acolloid particle (e.g., a hapten,alight-emitting substance, an antibody, an antigen, gold colloid, etc.),a metal, a metal ion, a metal chelate (e.g., trisbipyridine,trisphenanthroline, hexamine, etc.), or the like.

[0407] In the present invention, a sample to be tested or diagnosed isnot particularly limited and includes, for example, blood, serum,leukocytes, urine, stool, semen, saliva, tissue, cultured cells, sputum,and the like.

[0408] In one embodiment, a nucleic acid component is extracted fromthese samples in order to test nucleic acid. The extraction is notlimited to a particular method. A liquid-liquid extraction method, suchas phenol-chloroform method and the like, or a liquid-solid extractionmethod using a carrier can be used. Alternatively, a commerciallyavailable nucleic acid extraction method QIAamp (QIAGEN, Germany) or thelike can be used. Next, a sample containing an extracted nucleic acidcomponent is subjected to a hybridization reaction on a biomolecule chipof the present invention. The reaction is conducted in a buffer solutionhaving an ionic strength of 0.01 to 5 and a pH of 5 to 10. To thissolution may be added dextran sulfate (hybridization acceleratingagent), salmon sperm DNA, bovine thymus DNA, EDTA, a surfactant, or thelike. The extracted nucleic acid component is added to the solution,followed by heat denaturation at 90° C. or more. Insertion of abiomolecule chip can be carried out immediately after denaturation orafter rapid cooling to 0° C. Alternatively, a hybridization reaction canbe conducted by dropping a solution on a substrate. The rate of areaction can be increased by stirring or shaking during the reaction.The temperature of a reaction is in the range of 10° C. to 90° C. Thetime of a reaction is in the range of one minute to about one night.After a hybridization reaction, an electrode is removed and then washed.For washing, a buffer solution having an ionic strength of 0.01 to 5 anda pH of 5 to 10 can be used.

[0409] “Microcapsule” as used herein refers to a microparticleenveloping a substance with a molecular membrane or the like, or itscontainer-like substance. A microcapsule usually has a spherical shapeand a size of several micrometers to several hundred micrometers. Ingeneral, a microcapsule can be prepared as follows. A waterdroplet-in-water type emulsion is produced, and a polymer thin film isproduced by interfacial polycondensation at an interface between themicro-emulsion particle and a medium so that the particle is coveredwith the thin film. The capsule is isolated from the oil bycentrifugation, followed by dialysis for purification. When an emulsionis prepared, an intended biomolecule is dissolved and dispersed into awater phase, so that the biomolecule can be enveloped in a capsule. Thethickness of the thin film is 10 to 20 μm. The thin film can be providedwith semipermeability or surface charge. In the present invention, amicrocapsule protects and isolates a content, such as a biomolecule.Such a content can be optionally dissolved, mixed or allowed to react.In a method for producing a biomolecule substrate according to thepresent invention, a microcapsule is sprayed onto a substrate by an inkjet method (e.g., Bubble Jet®, etc.), a PIN method, or the like. Thesprayed microcapsule is heated to a temperature higher than the meltingpoint of its shell so that a content, such as a biomolecule, can beimmobilized on the substrate. In this case, the substrate is preferablycoated with a substance having an affinity for the biomolecule.

[0410] “Label” and “mark” as used herein have the same meaning and referto an entity which distinguishes an intended molecule or substance fromother substances (e.g., a substance, energy, electromagnetic wave,etc.). Examples of such a labeling method include an R1 (radioisotope)method, a fluorescence method, a biotin method, a chemiluminescencemethod, and the like. When both a nucleic acid fragment and itscomplementary oligonucleotide are labeled by a fluorescence method, theyare labeled with fluorescence substances having different maximumwavelengths of fluoresence. The difference in the maximum wavelength offluorescence is preferably at least 10 nm. Any fluorescence substancewhich can bind to a base portion of nucleic acid can be used. Preferablefluorescence substances include cyanine dye (e.g., Cy3, Cy5, etc. in CyDye™ series), a rhodamine 6G reagent, N-acetoxy-N-2-acetylaminofluorene(AAF), AAIF (an iodine derivative of AAF), and the like. Examples of acombination of fluorescence substances having a difference in themaximum wavelength of fluorescence of at least 10 nm, include acombination of Cy5 and a rhodamine 6G reagent, a combination of Cy3 andfluorescein, a combination of a rhodamine 6G reagent and fluorescein,and the like.

[0411] “Chip attribute data” as used herein refers to data associatedwith some information relating to a biomolecule chip of the presentinvention. Chip attribute data includes information associated with abiomolecule chip, such as a chip ID, substrate data, and biomoleculeattribute data. “Chip ID” as used herein refers to a code foridentification of each chip. “Substrate data” or “substrate attributedata” as used herein refers to data relating to a substrate used in abiomolecule chip of the present invention. Substrate data may containinformation relating to an arrangement or pattern of a biomolecule.“Biomolecule attribute data” refers to information relating to abiomolecule, including, for example, the gene sequence of thebiomolecule (a nucleotide sequence in the case of nucleic acid, and anamino acid sequence in the case of protein), information relating to agene sequence (e.g., a relationship between the gene and a specificdisease or condition), a function in the case of a low weight moleculeor a hormone, library information in the case of a combinatoriallibrary, molecular information relating to affinity for a low weightmolecule, and the like. “Personal information data” as used hereinrefers to data associated with information for identifying an organismor subject to be measured by a method, chip or apparatus of the presentinvention. When the organism or subject is a human, personal informationdata includes, but is not limited to, age, sex, health condition,medical history (e.g., drug history), educational background, thecompany of your insurance, personal genome information, address, name,and the like. When personal information data is of a domestic animal,the information may include data about the production company of theanimal. “Measurement data” as used herein refers to raw data as a resultof measurement by a biomolecule substrate, apparatus and system of thepresent invention and specific processed data derived therefrom. Suchraw data may be represented by the intensity of an electric signal. Suchprocessed data may be specific biochemical data, such as a blood sugarlevel and a gene expression level.

[0412] “Recording region” as used herein refers to a region in whichdata may be recorded. In a recording region, measurement data as well asthe above-described chip attribute data can be recorded.

[0413] In a preferable embodiment of the present invention, personalinformation data and biomolecule attribute data or measurement data maybe separately managed. By managing these data separately, the secrecy ofhealth-related information, i.e., personal privacy, can be protected.Moreover, in the case of medicament screening, even if screening isfarmed out to an outside company, data can be obtained without leakingto secret information to the outside company. Therefore, the presentinvention can be applied to outsourcing in which secret information isprotected.

[0414] (General Techniques)

[0415] Techniques as used herein are well known techniques commonly usedin microfluidics, micromachining, organic chemistry, biochemistry,genetic engineering, molecular biology, genetics, and their relatedfields with in the technical scope of the art, unless otherwisespecified. These techniques are sufficiently described in, for example,literature listed below and described elsewhere herein.

[0416] Micromachining is described in, for example, Campbell, S. A.(1996). The Science and Engineering of Microelectronic Fabrication,Oxford University Press; Zaut, P. V. (1996). MicromicroarrayFabrication: a Practical Guide to Semiconductor Processing,Semiconductor Services; Madou, M. J. (1997). Fundamentals ofMicrofabrication, CRC1 5 Press; Rai-Choudhury, P. (1997). Handbook ofMicrolithography, Micromachining, & Microfabrication: Microlithography;and the like, related portions of which are herein incorporated byreference.

[0417] Molecular biology and recombinant DNA techniques are describedin, for example, Maniatis, T. et al. (1982). Molecular Cloning: ALaboratory Manual, Cold SpringHarbor; Ausubel, F. M. (1987). CurrentProtocols in Molecular Biology, Greene Pub. Associates andWiley-Interscience; Ausubel, F. M. (1989). Short Protocols in MolecularBiology: A Compendium of Methods from Current Protocols in MolecularBiology, Greene Pub. Associates and Wiley-Interscience; Sambrook, J. etal. (1989). Molecular Cloning: A Laboratory Manual, Cold Spring Harbor;Innis, M. A. (1990). PCR Protocols: A Guide to Methods and Applications,Academic Press; Ausubel, F. M. (1992). Short Protocols in MolecularBiology: A Compendium of Methods from Current Protocols in MolecularBiology, Greene Pub. Associates; Ausubel, F. M. (1995). Short Protocolsin Molecular Biology: A Compendium of Methods from Current Protocols inMolecular Biology, Greene Pub. Associates; Innis, M. A. et al. (1995).PCR Strategies, Academic Press; Ausubel, F. M. (1999). Short Protocolsin Molecular Biology: A Compendium of Methods from Current Protocols inMolecular Biology, Wiley, and annual updates; Sninsky, J. J. et al.(1999). PCR Applications: Protocols for Functional Genomics, AcademicPress; and the like, related portions of which are herein incorporatedby reference.

[0418] Nucleic acid chemistry, such as DNA synthesis techniques and thelike, is described in, for example, Gait, M. J. (1985). OligonucleotideSynthesis: A Practical Approach, IRL Press; Gait, M. J. (1990).Oligonucleotide Synthesis: A Practical Approach, IRL Press; Eckstein, F.(1991). Oligonucleotides and Analogues: A Practical Approac, IRL Press;Adams, R. L. et al. (1992). The Biochemistry of the Nucleic Acids,Chapman & Hall; Shabarova, Z. et al. (1994). Advanced Organic Chemistryof Nucleic Acids, Weinheim; Blackburn, G. M. et al. (1996). NucleicAcids in Chemistry and Biology, Oxford University Press; Hermanson, G.T. (I 996). Bioconjugate Techniques, Academic Press; and the like,related portions of which are herein incorporated by reference.

[0419] Photolithography is a technique developed by Fodor et al., inwhich a photoreactive protecting group is utilized (see Science, 251,767(1991)). A protecting group for a base inhibits a base monomer of thesame or different type from binding to that base. Thus, a base terminusto which a protecting group is bound has no new base-binding reaction. Aprotecting group can be easily removed by irradiation. Initially, aminogroups having a protecting group are immobilized throughout a substrate.Thereafter, only spots to which a desired base is to be bound areselectively irradiated by a method similar to a photolithographytechnique usually used in a semiconductor process, so that another basecan be introduced by subsequent binding into only the bases in theirradiated portion. Now, desired bases having the same protecting groupat a terminus thereof are bound to such bases. Thereafter, the patternof a photomask is changed, and other spots are selectively irradiated.Thereafter, bases having a protecting group are similarly bound to thespots. This process is repeated until a desired base sequence isobtained in each spot, thereby preparing a DNA array. Photolithographytechniques may be herein used.

[0420] An ink jet method (technique) is a technique of projectingconsiderably small droplets onto a predetermined position on atwo-dimensional plane using heat or a piezoelectric effect. Thistechnique is widely used mainly in printers. In production of a DNAarray, an ink jet apparatus is used, which has a configuration in whicha piezoelectric device is combined with a glass capillary. A voltage isapplied to the piezoelectric device which is connected to a liquidchamber, so that the volume of the piezoelectric device is changed andthe liquid within the chamber is expelled as a droplet from thecapillary connected to the chamber. The size of the expelled droplet isdetermined by the diameter of the capillary, the volume variation of thepiezoelectric device, and the physical property of the liquid. Thediameter of the droplet is generally 30 μm. An ink jet apparatus usingsuch a piezoelectric device can expel droplets at a frequency of about10 KHz. In a DNA array fabricating apparatus using such an ink jetapparatus, the ink jet apparatus and a DNA array substrate arerelatively moved so that droplets can be dropped onto desired spots onthe DNA array. DNA array fabricating apparatuses using an ink jetapparatus are roughly divided into two categories. One category includesa DNA array fabricating apparatus using a single ink jet apparatus, andthe other includes a DNA array fabricating apparatus using a multi-headink jet apparatus. The DNA array fabricating apparatus with a single inkjet apparatus has a configuration in which a reagent for removing aprotecting group at a terminus of an oligomer is dropped onto desiredspots. A protecting group is removed from a spot, to which a desiredbase is to be introduced, by using the ink jet apparatus so that thespot is activated. Thereafter, the desired base is subjected to abinding reaction throughout a DNA array. In this case, the desired baseis bound to only spots having an oligomer whose terminus is activated bythe reagent dropped from the ink jet apparatus. Thereafter, the terminusof a newly added base is protected. Thereafter, a spot from which aprotecting group is removed is changed and the procedures are repeateduntil desired nucleotide sequences are obtained. On the other hand, in aDNA array fabricating apparatus using a multi-head ink jet apparatus, anink jet apparatus is provided for each reagent containing a differentbase, so that a desired base can be bound directly to each spot. A DNAarray fabricating apparatus using a multi-head ink jet apparatus canhave a higher throughput than that of a DNA array fabricating apparatususing a single ink jet apparatus. Among methods for fixing apresynthesized oligonucleotide to a substrate is a mechanicalmicrospotting technique in which liquid containing an oligonucleotide,which is attached to the tip of a stainless pin, is mechanically pressedagainst a substrate so that the oligonucleotide is immobilized on thesubstrate. The size of a spot obtained by this method is 50 to 300 μm.After microspotting, subsequent processes, such as immobilization usingUV light, are carried out.

BEST MODE FOR CARRYING OUT THE INVENTION

[0421] In one aspect, the present invention provides a method forfabricating a biomolecule substrate. This method comprises the stepsof: 1) providing a set of biomolecules and a substrate; 2) enclosing theset of biomolecules into microcapsules on thebiomolecule-type-by-biomolecule-type basis; and 3) spraying thebiomolecule microcapsules onto the substrate. Preferably, the set ofbiomolecules are uniform. In a preferred embodiment, the method providesa plurality of sets of biomolecules. Preferably, the microcapsules ofthe set of biomolecules of different types are disposed at differentpositions. In one embodiment, the present invention may further comprisethe step of washing the biomolecule microcapsules after the enclosingstep.

[0422] The spraying step used in the method of the present invention isperformed by an ink jet method (including a Bubble Jet® method), a PINmethod, or the like. Preferably, the spraying step may be performed by aBubble Jet® method. This is because the microcapsules may be efficientlyimmobilized.

[0423] In a preferred embodiment, the method may further comprise thestep of setting the temperature of a solution used in the spraying stepto be higher than the melting point of a shell of the biomoleculemicrocapsulate. Such an increased temperature of the solution can leadto efficient immobilization of the biomolecules.

[0424] In this biomolecule substrate fabrication method, the biomoleculemay be a naturally-occurring or synthetic biomolecule. Examples of sucha biomolecule include, but are not limited to, a protein, a polypeptide,an oligopeptide, a peptide, apolynucleotide, an oligonucleotide, anucleotide, nucleic acid (e.g., including DNA, such as cDNA or genomicDNA, and RNA, such as mRNA), a polysaccharide, an oligosaccharide,lipid, a low weight molecule (e.g., a hormone, a ligand, a signaltransduction substance, a low-weight organic molecule, etc.), andcomposite molecules thereof.

[0425] Preferably, the biomolecule substrate fabrication method of thepresent invention may further comprise the step of perform labelingspecific to each microcapsule.

[0426] In another aspect, the present invention provides a biomoleculechip. This biomolecule chip comprises: a substrate; and biomolecules andchip attribute data arranged on the substrate. The chip attribute datais arranged in the same region as that of the biomolecules. By placingthe biomolecules and the chip attribute data in the same region, anefficient testing can be perfomred.

[0427] In one embodiment, the above-described chip attribute data maycontain information relating to chip ID and the substrate. In anotherembodiment, the biomolecule chip of the present invention may furthercomprise a recording region, wherein the recording region is placed onthe same substrate as that of the biomolecule and the chip attributedata, and at least one of the subject data and measurement data isrecorded in the recording region. Preferably, both the subject data andmeasurement data may be recorded in the above-described recordingregion. Note that when it is intended to protect privacy depending onthe purpose, only a part of these pieces of information may be recordedin the recording region. In this case, such data may be encrypted andthen recorded.

[0428] Preferably, the above-described chip attribute data may berecorded in such a manner that the data can be read out by the samemeans as that for detecting the above-described biomolecule. Examples ofsuch detection means include, but are not limited to, any means capableof detecting the biomolecule, such as a fluorescence analysis apparatus,a spectrophotometer, a scintillation counter, and a luminometer. Sinceboth the chip attribute data and the biomolecule can be read out by thesame detection means, both testing of raw data and reading ofmeasurement conditions can be performed by a single read-out operation,thereby making it possible to significantly reduce an operation time andsimplifying signal sending and receiving equipment.

[0429] In a preferred embodiment, a specific mark may be attached to theabove-described substrate. By attaching the specific mark to thesubstrate, identification of the substrate can be double-checked,thereby making it possible to reduce diagnosis and testing errors. Inanother preferred embodiment, the specific mark is arranged based on thechip attribute data. By providing such a specific mark, it is possibleto easily read out chip attribute data.

[0430] In another embodiment, the above-described chip attribute datamay contain the above-described biomolecule attribute data. By addingthe biomolecule attribute data to the biomolecule chip, various testsand diagnoses can be performed by using only the chip. In anotherembodiment, this chip attribute data can be maintained in another site.By maintaining the data in another site, personal information can beprevented from being unintentionally leaked even when the biomoleculechip is unintentionally passed to a third party.

[0431] In another embodiment, information relating to an address of theabove-described biomolecule may be further recorded. Examples of suchaddress information include geometric information of an arrangement or apattern defined in the present invention. By adding address-relatedinformation to the biomolecule chip, a stand-alone test can beperformed. The address-related information can also be maintained inanother site. By maintaining the information in another site, personalinformation can be prevented from being unintentionally leaked even whenthe biomolecule chip is unintentionally passed to a third party. In apreferred embodiment, the address may be a tracking address.

[0432] In a further preferred embodiment, the above-described chipattribute data may be encrypted. The whole or a part of the data may beencrypted. Preferably, personal information data, biomolecule attributedata, and measurement data may be encrypted. These data may be encryptedby separate encryption means. Such an encryption means is well known inthe art, including, for example, a means using a public key. The presentinvention is not so limited.

[0433] In another embodiment, data relating to a label used to detectthe biomolecule may be recorded. Examples of such a label include, butare not limited to, any substance for labeling a biomolecule, such as,for example, a fluorescent molecule, a chemoluminescent molecule, aradioactive isotope, and the like. By providing such label-related data,a test or diagnosis can be performed by using only a biomolecule chip.Preferably, the label-related data contains at least one of thewavelength of excited light and the wavelength of fluorescence, and morepreferably both of them.

[0434] The biomolecule used in the biomolecule chip of the presentinvention may be a naturally-occurring or synthetic biomolecule.Examples of such a biomolecule include, but are not limited to, aprotein, a polypeptide, an oligopeptide, a peptide, apolynucleotide, anoligonucleotide, a nucleotide, nucleic acid (e.g., including DNA, suchas cDNA or genomic DNA, and RNA, such as mRNA), a polysaccharide, anoligosaccharide, lipid, a low weight molecule (e.g., a hormone, aligand, a signal transduction substance, a low-weight organic molecule,etc.), and composite molecules thereof. Preferably, the biomolecule maybe a nucleic acid or a protein, and more preferably DNA (e.g., cDNA orgenomic DNA). In another preferred embodiment, the biomolecule may beDNA amplified by an amplification means, such as PCR or the like. Inanother preferred embodiment, the biomolecule may be a synthesizedprotein.

[0435] In another aspect, the present invention provides a biomoleculechip comprising: 1) a substrate; and 2) biomolecules arranged on thesubstrate, wherein spots of the biomolecules are spaced by at least onenon-equal interval, an address of the biomolecule spot can be identifiedfrom the non-equal interval. By providing at least one non-equalinterval, the interval can be used as a reference to identify therelative positions of other spots. With this structure, it is possibleto identify the address of a spot having interaction only by the stepsof detecting all biomolecules and detecting a spot after contacting asample, without a step of identifying the position of the spot. Such anaddress identifying method is also herein called address identificationusing specific “arrangement”. FIG. 47 shows an example of addressspecification using specific arrangement. In FIG. 47, biomolecules arespaced at equal intervals as indicated by 302, except that at least oneinterval between biomolecules is a non-equal interval as indicated by303. When this non-equal interval is used as a starting point, theaddress of any spot can be identified.

[0436] Preferably, the non-equal interval is modulated. Modulation asused herein refers to variations in spot interval. Modification may beeither regular or irregular. An example of such modulation is a sequenceof 00, 01, 10, 00, 01, 01, 01 in the binary number system. The presentinvention is not so limited. By changing modulation, more efficientaddress identification can be made possible.

[0437] In a certain embodiment, the above-described non-equal intervalsmay be present in at least two directions. Preferably, the non-equalintervals in the two directions may be distinguished from each other. Byusing the non-equal intervals in at least two directions, address can bereliably identified even if data is read out in the case when thesubstrate is turned upside down. Preferably, a plurality of suchnon-equal intervals may be present. Moreover, such non-equal intervalscan be scattered on a substrate.

[0438] In another embodiment, the present invention provides abiomolecule chip comprising: 1) a substrate: and 2) biomoleculesarranged on the substrate, wherein the biomolecules include adistinguishable first biomolecule and a distinguishable secondbiomolecule, an address of the biomolecule can be identified based on anarrangement of spots of the first biomolecules and spots of the secondbiomolecule. By providing at least two types of distinguishablebiomolecules, it is possible to identify the address of a spot havinginteraction only by the steps of detecting all biomolecules anddetecting a spot after contacting a sample, without a step ofidentifying the position of the spot. Such an address identifying methodis also called address identification using a specific “pattern”. FIG.48 shows an example of address identification using a specific pattern.In FIG. 48, a first biomolecule 311 can be distinguished from a secondbiomolecule 312. In this example, by using the second biomolecule 312 asa starting point, the address of any spot can be identified.

[0439] “Distinguishable” as used herein indicates that identificationcan be carried out by at least one detection means (including, notlimited to, the naked eye, a fluorescence measurement apparatus, aspectrophotometer, a radiation measurement apparatus, etc.). Therefore,a distinguishable biomolecule may be, for example, a molecule which canbe identified by the naked eye, or a molecule which emits differentfluorescence when it is excited. “Distinguishable” also indicates thatidentification can be carried out by the same label having a differentlevel (e.g., a difference in the amount of dye, etc.).

[0440] In one embodiment of the biomolecule chip of the presentinvention in which an address is identified by a specific arrangement ora specific pattern, a label distinguishable from the biomolecule may beplaced between the biomolecule spots. Such a label may be any label asdefined herein, and preferably a label which can be detected by the samedetection means as the above-described means for detecting abiomolecule.

[0441] In one embodiment of the biomolecule chip of the presentinvention in which an address is identified by a specific arrangement ora specific pattern, the above-described distinguishable label can bedetected by a detection means. Examples of such detection means include,but are not limited to, any means capable of detecting the biomolecule,such as a fluorescence analysis apparatus, a spectrophotometer, ascintillation counter, and a luminometer.

[0442] In one embodiment of the biomolecule chip of the presentinvention in which an address is identified by a specific arrangement ora specific pattern, the label may be arranged in a horizontal directionand a vertical direction on the substrate.

[0443] In one embodiment of the biomolecule chip of the presentinvention in which an address is identified by a specific arrangement ora specific pattern, a synchronization mark may be arranged. By providinga synchronization mark, address identification is made easier.

[0444] A biomolecule used in one embodiment of the biomolecule chip ofthe present invention in which an address is identified by a specificarrangement or a specific pattern may be a naturally-occurring orsynthetic biomolecule. Examples of such a biomolecule include, but arenot limited to, a protein, a polypeptide, an oligopeptide, a peptide, apolynucleotide, an oligonucleotide, a nucleotide, nucleic acid (e.g.,including DNA, such as cDNA or genomic DNA, and RNA, such as mRNA), apolysaccharide, an oligosaccharide, lipid, a low weight molecule (e.g.,a hormone, a ligand, a signal transduction substance, a low-weightorganic molecule, etc.), and composite molecules thereof. Preferably,the biomolecule may be a nucleic acid or a protein, and more preferablyDNA (e.g., cDNA or genomic DNA). In another preferred embodiment, thebiomolecule may be DNA amplified by an amplification means, such as PCRor the like.

[0445] In another aspect, the present invention provides a biomoleculechip. This biomolecule chip comprises: 1) a substrate; and 2)biomolecules arranged on the substrate, wherein spots storing attributedata are arranged on a side of the substrate opposite to a side on whichspots of the biomolecules are arranged. By arranging the spots storingattribute data on the rear side of the biomolecule chip, both data canbe detected by a single read-out operation so that testing and/ordiagnosis can be performed. Preferably, this attribute data may containaddress information. The attribute data may contain biomoleculeattribute data and the like.

[0446] In another aspect, the present invention provides a biomoleculechip comprising: 1) a substrate; 2) biomolecules arranged on thesubstrate; and 3) a data recording region. By providing such a datarecording region, it is possible to perform testing and/or diagnosisusing only a biomolecule chip. Preferably, the data recording region maybe placed on a side of the substrate opposite to a side on which spotsof the biomolecules are arranged.

[0447] In one aspect, the present invention provides a method fordetecting a label of a biomolecule chip. This method comprises the stepsof: 1) providing a biomolecule chip on which at least one labeledbiomolecule is arranged; 2) switching detection elements sequentiallyfor detecting the biomolecules on the biomolecule chip; and 3)identifying a signal detected by the detection element. With thismethod, a signal can be detected efficiently and in real time in abiomolecule chip. Preferably, this method further comprise: 4) adding upeach detected signal. In one embodiment, this signal may be separatedusing a wavelength separation mirror. In another embodiment, theabove-described biomolecule substrate may further comprise asynchronization mark, and the label may be identified based on thesynchronization mark. By providing the synchronization mark, an addresscan be smoothly identified. In another embodiment, the biomoleculesubstrate contains address information on a rear side of thebiomolecule, and the label is identified based on the addressinformation.

[0448] In another aspect, the present invention provides a method fortesting information from an organism. This method comprises the stepsof: 1) providing a biomolecule sample from the organism; 2) providing abiomolecule chip of the present invention; 3) contacting the biomoleculesample to the biomolecule chip, and placing the biomolecule chip underconditions which causes an interaction between the biomolecule sampleand a biomolecule placed on the biomolecule; and 4) detecting a signalcaused by the biomolecule and a signal caused by the interaction,wherein the signal is an indicator for at least one informationparameter of the organism, and the signal is related to an addressassigned to the non-equal interval or the spot arrangement.

[0449] In a preferred embodiment of the method of the present inventionfor testing information on an organism, the sample contains a proteinand the biomolecule placed on the biomolecule chip is an antibody, orthe sample contains an antibody and the biomolecule placed on thebiomolecule chip is a protein. In this detection method, hybridizationbetween nucleic acids is detected. This hybridization may be performedunder various stringency conditions. When SNP is detected, stringenthybridization conditions maybe used. When a gene having a relationshipbut being far with respect to species is searched for, moderatehybridization conditions may be used. Such hybridization conditions canbe determined by those skilled in the art from the well-known routinetechniques, depending on the situation.

[0450] In a preferred embodiment of the method of the present inventionfor testing information on an organism, the sample contains a proteinand the biomolecule placed on the biomolecule chip is an antibody, orthe sample contains an antibody and the biomolecule placed on thebiomolecule chip is a protein. In this detection method, anantigen-antibody reaction is detected. An antigen-antibody reaction maybe detected under various stringency conditions. The antibody may beeither a monoclonal antibody or polyclonal antibody. Preferably, theantibody may be a monoclonal antibody. The antibody may be a chimeraantibody, a humanized antibody, or the like.

[0451] In a preferred embodiment, the method of the present inventionfurther comprises labeling the biomolecule sample with a label molecule.By labeling a sample with a desired label molecule, a desired detectionmeans can be used.

[0452] In a preferred embodiment of the method of the present inventionfor testing information on an organism, the label molecule may bedistinguished from the biomolecule placed on the biomolecule chip. Byproviding a label which can be distinguished from a biomolecule, it iseasy to detect a spot in which an interaction occurs. The label whichcan be distinguished from a biomolecule refers to a label which can bedistinguished from a biomolecule by at least one detection means asdescribed above.

[0453] In a preferred embodiment of the method of the present inventionfor testing information on an organism, the above-described labelmolecule contains a fluorescent molecule, a photophorescent molecule, achemoluminescent molecule, or a radioactive isotope. In this case, adetection means corresponding to the type of label molecule may be used.

[0454] In a preferred embodiment of the method of the present inventionfor testing information on an organism, the signal detecting step may beperformed either at a site different from where the interaction occursor at the same site as where the interaction occurs. When the signaldetecting step is performed at a different site, the signal may beencrypted. Such encryption is well known in the art. For example,encryption using a public key may be used. By performing detection at adifferent site, it maybe possible to outsource diagnosis or testing.

[0455] In a preferred embodiment of the method of the present inventionfor testing information on an organism, the method may further comprisesubjecting the signal to filtering so as to extract only signalsrelating to required information. This step may be required forprotecting personal information when outsourcing testing.

[0456] In another aspect, the present invention provides a method fordiagnosing a subject. The method comprises the steps of: 1) providing asample from the subject; 2) providing a biomolecule chip of the presentinvention; 3) contacting the biomolecule sample to the biomolecule chip,and placing the biomolecule chip under conditions which causes aninteraction between the biomolecule sample and a biomolecule placed onthe biomolecule; 4) detecting a signal caused by the biomolecule and asignal caused by the interaction, wherein the signal is at least onediagnostic indicator for the subject, and the signal is related to anaddress assigned to the non-equal interval or the spot arrangement; and5) determining the diagnostic indicator from the signal.

[0457] In a preferred embodiment of the method of the present inventionfor testing information on an organism, the sample is nucleic acid, andthe biomolecule placed on the biomolecule chip is nucleic acid. In thisdetection method, hybridization between nucleic acids is detected. Thishybridization may be performed under various stringency conditions. WhenSNP is detected, stringent hybridization conditions may be used. Byplacing nucleic acid relating to a specific disease on a biomoleculechip, a singnal caused by hybridization may be an indicator for thespecific disease.

[0458] In a preferred embodiment of the method of the present inventionfor testing information on an organism, the sample contains a proteinand the biomolecule placed on the biomolecule chip is an antibody, orthe sample contains an antibody and the biomolecule placed on thebiomolecule chip is a protein. In this test method, an antigen-antibodyreaction is detected. The antigen-antibody reaction may be detectedunder various stringency conditions. By placing a protein or an antibodyrelating to a specific disease or condition on a biomolecule chip, adetected signal may be an indicator relating to the specific disease orcondition.

[0459] In a preferred embodiment of the method of the present inventionfor testing information on an organism, the method further compriseslabeling the sample with a label molecule. By labeling a sample with adesired label, a desired detection means can be used. The label moleculemaybe distinguishable from a biomolecule placed on the above-describedbiomolecule chip. By providing a label which can be distinguished from abiomolecule, it is easy to detect a spot having an interaction.

[0460] In a preferred embodiment of the method of the present inventionfor testing information on an organism, the above-described labelmolecule may contain a fluorescent molecule, a phosphorescent molecule,a chemoluminescent molecule, or a radioactive isotope. In this case, adetection means corresponding to the type of the label molecule may beused.

[0461] In a preferred embodiment of the method of the present inventionfor testing information on an organism, the diagnostic indicator may bean indicator for a disease or a disorder. In another embodiment, thediagnostic indicator may be based on single nucleotide polymorphism(SNP). This diagnostic indicator may be related to a genetic disease. Inanother embodiment, the diagnostic indicator may be based on theexpression level of a protein. The diagnostic indicator may be based ona test result of a biochemical test. A plurality of test values based onthe biochemical tests may be used.

[0462] In a preferred embodiment of the method of the present inventionfor testing information on an organism, the determining step may beperformed either at a site different from where the interaction occursor at the same site as where the interaction occurs. When thedetermining step is performed at a different site, the present inventionmay further comprise encrypting the signal. By performing detection at adifferent site, it maybe possible to outsource diagnosis or testing.Such outsourcing corresponds to industrially applicable work.

[0463] In a preferred embodiment of the method of the present inventionfor testing information on an organism, the method may further comprisesubjecting the signal to filtering so as to extract only signalsrelating to required information. This step may be required for avoidingexcessive leakage of personal information to protect the personalinformation when outsourcing testing.

[0464] In a preferred embodiment of the method of the present inventionfor testing information on an organism, in the detecting stepbiomolecule attribute data is hidden, and in the determining steppersonal information data is hidden. Thereby, the whole informationrequired for diagnosis is prevented from being concentrated into aperson or entity, whereby personal information can be protected.

[0465] In another aspect, the present invention provides a testapparatus information on an organism. This apparatus comprises: 1) abiomolecule chip of the present invention; 2) a sample applying sectionin fluid communication with the biomolecule chip; 3) a reaction controlsection for controlling a contact and an interaction between thebiomolecule placed on the biomolecule and a biomolecule sample appliedfrom the sample applying section; and 4) a detection section fordetecting a signal caused by the interaction, wherein the signal is anindicator for at least one information parameter of the organism, andthe signal is related to an address assigned to the non-equal intervalor the spot arrangement. This apparatus can perform testing ofbiological information without additional address identification.

[0466] In a preferred embodiment, the test apparatus of the presentinvention further comprises a section for receiving and sending thesignal. By providing the section for receiving and sending the signal,it is possible to send or receive information to or from the outside.This sending and receiving section may be connected to a recordingapparatus drive, such as a flexible disk drive, an MO drive, a CD-Rdrive, a DVD-R drive, or a DVD-RAM drive; or a network, such as theInternet or an intranet.

[0467] In a preferred embodiment, the test apparatus of the presentinvention further comprises a region for recording the signal. Byproviding the recording region, it is possible to store a result of atest. When the test apparatus is used a plurality of times, stored testresults can be compared with each other.

[0468] In another aspect, the present invention provides a diagnosisapparatus for a subject. The apparatus comprises: 1) a biomolecule chipof the present invention; 2) a sample applying section in fluidcommunication with the biomolecule chip; 3) a reaction control sectionfor controlling a contact and an interaction between the biomoleculeplaced on the biomolecule and a biomolecule sample applied from thesample applying section; 4) a detection section for detecting a signalcaused by the biomolecule and a signal caused by the interaction,wherein the signal is an indicator for at least one informationparameter of the organism, and the signal is related to an addressassigned to the non-equal interval or the spot arrangement; and 5)determining the diagnostic indicator from the signal. This apparatus canperform testing of subject information without additional addressidentification.

[0469] In a preferred embodiment, the test apparatus of the presentinvention further comprises a section for receiving and sending thesignal. By providing the section for receiving and sending the signal,it is possible to send or receive information to or from the outside.This sending and receiving section may be connected to a recordingapparatus drive, such as a flexible disk drive, an MO drive, a CD-Rdrive, a DVD-R drive, or a DVD-RAM drive; or a network, such as theInternet or an intranet.

[0470] In a preferred embodiment, the test apparatus of the presentinvention further comprises a region for recording the signal. Byproviding the recording region, it is possible to store a result ofdiagnosis. When the test apparatus is used a plurality of times, storeddiagnosis results can be compared with each other.

[0471] In another aspect, A biological test system, comprising: A) amain sub system, comprising: 1) a biomolecule chip of the presentinvention; 2) a sample applying section in fluid communication with thebiomolecule chip; 3) a reaction control section for controlling acontact and an interaction between the biomolecule placed on thebiomolecule and a biomolecule sample applied from the sample applyingsection; 4) a detection section for detecting a signal caused by thebiomolecule and a signal caused by the interaction, wherein the signalis an indicator for at least one information parameter of the organism,and the signal is related to an address assigned to the non-equalinterval or the spot arrangement; and 5) a sending and receiving sectionfor sending and receiving a signal, and B) a sub sub system,comprising: 1) a sending and receiving section for sending and receivinga signal; and 2) a test section for calculating a test value from thesignal received from the main sub system, wherein the main sub systemand the sub sub system are connected together via a network.

[0472] Preferably, the main sub system and the sub sub system areconnected together via a network.

[0473] In another preferred embodiment, the signal received by the subsub system contains a signal relating to measurement data measured bythe sub sub system.

[0474] More preferably, the attribute data contains chip ID, personalinformation data, and biomolecule attribute data; the main sub systemcontains the chip ID and the personal information data, but does notcontain the biomolecule attribute data; and the sub sub system containsthe chip ID and the biomolecule attribute data, but does not contain thepersonal information data, and the sub sub system sends the test value,determined in response to a request, to the main sub system. Therefore,the biological test system of the present invention prevents leakage ofinformation to a third party. If information is leaked, privacy can beprotected in testing an organism. In a preferred embodiment, the signalto be sent and received is encrypted.

[0475] Preferably, the above-described network may be the Internet orother networks (e.g., an intranet, etc.).

[0476] In another aspect, the present invention provides a diagnosissystem comprising: A) a main sub system, comprising: 1) the biomoleculechip of the present invention; 2) a sample applying section in fluidcommunication with the biomolecule chip; 3) a reaction control sectionfor controlling a contact and an interaction between the biomoleculeplaced on the biomolecule and a biomolecule sample applied from thesample applying section; 4) a detection section for detecting a signalcaused by the biomolecule and a signal caused by the interaction,wherein the signal is an indicator for at least one informationparameter of the organism, and the signal is related to an addressassigned to the non-equal interval or the spot arrangement; and 5) asending and receiving section for sending and receiving a signal, and B)a sub sub system, comprising: 1) a sending and receiving section forsending and receiving a signal; and 2) a determination section fordetermining the diagnostic indicator from the signal received from themain sub system. The main sub system and the sub sub system areconnected together via a network. In a preferred embodiment, the signalto be sent and received is encrypted.

[0477] Preferably, the signal received by the sub sub system contains asignal relating to measurement data measured by the sub sub system. Morepreferably, the attribute data contains chip ID, personal informationdata, and biomolecule attribute data, the main sub system contains thechip ID and the personal information data, but does not contain thebiomolecule attribute data, and the sub sub system contains the chip IDand the biomolecule attribute data, and data for determining adiagnostic indicator from biomolecule attribute data, but does notcontain the personal information data, and the sub sub system sends thediagnostic indicator, determined in response to a request, to the mainsub system. Therefore, the diagnosis system of the present inventionprevents leakage of information to a third party. If information isleaked, privacy can be protected in diagnosis.

[0478] Preferably, the above-described network may be the Internet orother networks (e.g., an intranet, etc.).

[0479] In another aspect, A test apparatus for biological informationcomprising: a support for a substrate; a plurality of groups ofbiomolecules arranged on the substrate, each group containing thebiomolecules of the same type; shifting means for shifting thesubstrate; a light source for exciting a fluorescence substance labelinga sample to be tested; and optical means for converging light from thelight source. The light source is caused to emit light intermittently inresponse to an intermittent emission signal so as to excite thefluorescence substance, fluorescence from the fluorescence substance isdetected by a photodetector during a period of time when theintermittent emission signal is paused, identification information isreproduced from an arrangement of the DNAs, and the biomoleculesemitting fluorescence is identified.

[0480] Preferably, the test apparatus further comprises means for addingup detected detection signals. In another preferred embodiment, the testapparatus further comprises a wavelength separation mirror.

[0481] In another aspect, the present invention provides use of abiomolecule chip of the present invention for fabricating an apparatusfor testing biological information.

[0482] In another aspect, the present invention provides use of abiomolecule chip of the present invention for fabricating an apparatusfor diagnosing a subject.

[0483] In still another aspect, the present invention provides use of abiomolecule of the present invention for screening for a medicament andfabricating an apparatus for screening for a medicament. The presentinvention also provides a biomolecule chip for medicament screening. Thepresent invention also provides a screening apparatus for medicamentscreening. The present invention also provides a method for screeningfor a medicament using a biomolecule chip of the present invention.These method, apparatus, and biomolecule chip have a fundamentalstructure constructed by the same principle as that of testing anddiagnosis for a biomolecule, which can be implemented by those skilledin the art with reference to the present specification.

[0484] Hereinafter, the present invention will be described by way ofexamples illustrating best mode embodiments. Examples described beloware only for illustrative purposes. Therefore, the scope of the presentinvention is limited only by the scope of the claims, but not to theexamples.

EXAMPLES

[0485] Hereinafter, best mode embodiments of the present invention willbe described by way of examples with reference to FIGS. 1 to 46.

Example 1 Fabrication Example of Biomolecule Chip (1)

[0486] In this example, a method for arranging and immobilizing captureDNAs 2 having different sequences on a substrate 1 will be described.

[0487]FIG. 1(a) is a top view of DNA spots 2 in which a group of DNAfragments having a specific sequence are fixed on the substrate 1 in theshape of a dot according to the present invention. FIG. 1(b) is across-sectional view thereof. The substrate 1 is usually made of glassand may be made of a plastic. The shape of the substrate 1 may be asquare like a DNA chip, or a circle. DNA dots 2 each contain a differentcapture DNA which is immobilized on the substrate 1. The size of the DNAdot is 100 to 200 μm in diameter in the case of a microarray, and 10 to30 μm in the case of a DNA chip.

[0488] A method for forming DNA spots will be described with referenceto FIGS. 2 and 3. As shown in FIG. 2, (1) shows a capture DNA 3. Amethod of preparing capture DNA is omitted. The capture DNA and labeledDNA with a subject label are subjected to hybridization so as to predictthe sequence of subject DNA. (2) shows a DNA solution 4 containing thecapture DNA 3. (3) shows a DNA microcapsule 6 in which the DNA solution4 is covered with a covering 5. (4) shows a container 11 in which theDNA microcapsule 6 is dispersed in a solution 8. (5) shows amicrocapsule 9 in which the DNA microcapsules 6 shown in (4) arecollected and enveloped together with the solution 8 with asub-membrane.

[0489] This microcapsulation makes it possible to select separately twosolutions, i.e., the main solution 4 of DNA and the sub-solution 8 ofthe DNA microcapsule. As the DNA solution 4, a solution optimal to DNAor a solution required to immobilize the DNA 3 to the substrate 1 can beselected. As the sub-solution 8, a solution having an optimal viscosityor washing attachability when DNA is arranged on the substrate 1 in aPIN method or an ink jet method can be selected.

[0490]FIG. 3 shows a method for arranging 1^(st) to K^(th) DNA spots onthe substrate 1 by a pinning spot method. Initially, on a tray 12,several hundreds to several thousands of containers 11 (FIG. 2(4))containing capture DNA having a different sequence are arranged in theorder of DNA numbers. As shown in FIGS. 4(1), (2), (3) and (4), at (1) amoving pin 14 is moved so that the DNA microcapsule can be attached tothe moving pin 14 from the DNA container 11; at (2) and (3) the DNAmicrocapsule solution is attached to a tip of a pin 13; at (4) themoving pin 14 is washed in a washing section 15, n^(th) DNA is removed,and thereafter, n+1^(th) DNA is attached to the moving pin 14. Returningto FIG. 3, 1^(st) to K^(th) DNAs are attached one after another to thepins 13 on a pin drum 16, being spaced at specific intervals.

[0491] The attached DNAs are then attached to the substrate 1 one afteranother as the pin drum 16 is rotated. The DNAs 3 are thus placed on thesubstrate 1. Assuming that a half of the minimum DNA interval is definedas t, FIG. 3 illustrates that DNAs are spaced by intervals 1t, 2t, 3t,and 5t.

[0492] Immobilization of DNA in the attached DNA microcapsule 6 and thesub-solution 8, i.e., immobilization of capture DNA onto the substrate1, will be described with reference to FIG. 7. As shown in FIG. 7(1),the DNA microcapsule 6 and the sub-solution 4 are attached onto thesubstrate 1. The vaporization temperature of sub-solution 4 is lowerthan the melting point of a membrane 6. Therefore, when the temperatureis slightly increased at (2), the sub-solution 4 is evaporated, leavingonly the microcapsule 6. When the temperature is further increased at(3) to the melting point of the membrane 6, the membrane 6 is melted sothat the fluid of the melted membrane 6, the main solution 4, and thecapture DNA 3 are mixed to a solution. In this case, the membrane 6 maybe made of a material whose vaporization temperature is lower than thevaporization temperature of the main solution and the membrane 6 may beevaporated. A surface of the substrate 1 has been subjected to surfacetreatment so that DNA is easily immobilized on the surface. Therefore,at (4) the capture DNA 3 is immobilized on the substrate 1 as shown inFIG. 8. A part or the whole of the main solution 4 is dried at (5) andwashed at (6), thereby completing the DNA spot 2.

[0493] In the present invention, arrangement of DNA spots 2 a, 2 b, and2 a is modulated so as to incorporate positional information thereinto.According to this positional information, the positional orders of therespective DNA spots 2 can be determined. At the same time, as shown inFIG. 5, a DNA spot region 17 and a data region 18 are separated fromeach other. In the data region, a substrate ID 19, a DNA numbercorrespondence table 20 for the position of a DNA spot and a DNA spotID, and the sequence data 21 of DNA itself (biomolecule attribute data)(data structure shown in FIG. 5(2)) are modulated and recorded in a dotpattern. The dot pattern can be read by an XY scanner. Therefore, thearrangement data of DNA spots can be read by an XY scanner.Alternatively, data in the data region can be read out using anexcitation laser for allowing a sample to generate fluorescence. FIG. 6shows a specific example of DNA substrate attribute data. DNA substrateID 19, a DNA number-position correspondence table 20 indicating thecorrespondence between DNA numbers and positional information, and DNAsequence data 21 indicating the DNA sequence of each DNA, has beenrecorded as data in the data region before shipment from the factory.Note that the DNA sequence data of a DNA number is encrypted using anencryption key and then recorded. Personal DNA data is information of ahigh level of personal privacy which has to be stringently protected,and therefore, is encrypted using a public key, such as RSA, ellipsecode, or the like, or a high-bit encryption key. Therefore, even if aDNA chip or a DNA substrate containing subject information is run off,the DNA sequence of a specific DNA spot cannot be read without anencryption key. Therefore, personal DNA information can be preventedfrom leaking. It is also conceivable to accumulate DNA sequence data 21in a DNA management center without recording the data in DNA chips inorder to improve security. The user informs a DNA management center of aDNA substrate ID 19 and a reaction between labeled DNA 22 and a DNA spot2, i.e., fluorescence level data. Next, the center searches a DNAsubstrate database for the DNA sequence of each DNA spot using the DNAsubstrate ID 19. The center further analyzes a reaction result of a DNAspot and labeled DNA 22, DNA sequence-disease correspondence data todiagnose and predict a disease (in the case of a human), and sends onlynecessary information to laboratory medical technologist or a doctor inencrypted form. With this system, privacy information is prevented fromimproperly leaking.

Example 2 Fabrication Example of Biomolecule Chip (2): Ink Jet Method

[0494] The pin spot method has been described above. Next, a method ofattaching DNA to a substrate using ink jet will be described. FIG. 9 isa block diagram showing an ink jet (Bubble Jets) attaching apparatus. Anink jet nozzle 24 contains microcapsules 9 a, 9 b containing DNA andempty microcapsules 23 a, 23 b, 23 c, 23 d containing only main solution4, which are supplied from an ink supplying section 25. A specific emptycapsule contains a specific dye for indicating address information. Amaster control section 28 sends an eject command to an eject signalgeneration section 29 and then an eject control circuit 27. As a result,an eject section 26 generates heat so that bubbles occur. The bubblescause the microcapsule 9 a to be ejected toward a substrate. The emptymicrocapsules 23 b, 23 c are ejected. However, the empty microcapsules23 b, 23 a are unnecessary. When a photodetector 31 detects an emptymicrocapsule, a removal signal generation section 30 sends a removalsignal to an unnecessary liquid removing section 32. In the unnecessaryliquid removing section 32, a deviation field is applied to a deviationsection 33 so that unnecessary liquid in the empty microcapsule 23 isremoved as indicated by dashed-line arrow 34 and does not reach asubstrate.

[0495] The photodetector 31 has color filters 31 g, 31 h, 31 i (R, G, B,etc.), and therefore, can detect the color information of an emptymicrocapsule. The photodetector 31 also has a counter section 111. Afirst counter 111 a counts the number of microcapsule blocks. A secondcounter 111 b counts the number of DNA microcapsules. A third counter111 c counts the number of empty microcapsules. When there are fourcolors, 2-bit address data is obtained from a set of emptymicrocapsules. 16-bit address data is obtained from 8 emptymicrocapsules. When two bit of the 16 bits are used as check bits, it ispossible to precisely check if the order, arrangement, or number ofmicrocapsules is incorrect. Therefore, incorrect attachment can beadvantageously prevented. Even when microcapsules are not colored, 2bits can be obtained by ejecting 1, 2, 3, or 4 microcapsulesconsecutively. When 8 sets are used, 16 bits can be obtained, i.e., thesame size of address data as above can be obtained. The addressinformation of a microcapsule obtained by the photodetector 31 is sentvia an address output section 31 p to the master control section. DNAnumber can be identified based on address information. For example, asshown in step 68 m in a flowchart of FIG. 15, if a microcapsule makesthe number of DNA capsules having DNA number n greater by one, a removalsection described below removes the microcapsule.

[0496] On the other hand, the substrate 1 is moved by a predeterminedamount by a shift section 37 controlled by a shift amount controlcircuit 36 based on a signal from a shift amount detector 35, so thatDNA spots 2 a to 2 h are attached onto the substrate 1 as shown in FIG.10(4).

[0497] Next, the flowchart of FIG. 15 will be described. Initially, step68 a sets m=0, n=1. If a synchronization capsule sequence is detected atstep 68 b, a capsule block number m of the first counter 111 a isincreased by one in step 68 c. Whether or not m is the last number ischecked in step 68 d. The arrangement and order of empty microcapsulesin m^(th) block are checked in step 68 f. If a result of step 68 g isincorrect, the process goes to step 68 m. If the number of microcapsulesis greater by L than a reference number, an eject signal (=1) is outputin step 68 n for L capsules. A removal signal (=1) is output so as toremove a capsule. This operation is carried out L times to cause thearrangement to be normal and the process then returns to step 68 g. If aresult of step 68 m is NO, the process goes to step 68 p. If the numberof microcapsules is smaller by L than the reference value, ejection isstopped for clocks corresponding to L microcapsules in step 68 q. Duringthis time, DNA spot 2 is missing. Therefore, a defect block flag is setto be 1, which is recorded in the data region 18 on the DNA substrate 2,indicating the presence of the defect. The address of a microcapsule inan address counter 112 or an address block counter 113 is corrected byincreasing the address by L.

[0498] Now, the process returns to step 68 g. The number of DNAmicrocapsules is checked in step 68 h. If the result is OK, the ejectsignal is set to be ON and the removal signal is set to be OFF for oneunit in step 68 i. In this case, microcapsules are ejected so that oneDNA spot is formed. In this case, it is judged that there is no defect,and the address for a DNA microcapsule is increased by one(step 68 k).The process then returns to step 68 b. Thus, DNA spots 2, which containcorresponding DNA, can be formed.

[0499] Now, an ejection procedure using ink jet will be described withreference to FIG. 11. In (1), (2), the microcapsule 9 a containing nthDNA reaches the tip of the nozzle 24. When a voltage is applied to theeject section 26 in (2), a bubble is generated so that the microcapsule9 a is ejected in (3) and is attached to the substrate 1 in (4). Thismethod is called Bubble Jet®. A piezoelectric device may be providedinstead of the eject section 26 to obtain the same effect. In this case,by applying an eject voltage to the piezoelectric device, a microcapsuleis ejected in a piezoelectric ink jet method. Meanwhile, themicrocapsule 9 b containing (n+1)^(th) DNA reaches the tip portion. Whenan eject voltage is applied in (5), the microcapsule 9 b is ejectedtoward the substrate 1. In (6), (n+2)^(th) microcapsule 9 c istransported to the tip portion. In this case, the empty microcapsules 23d, 23 e among the three consecutive empty microcapsules 23 a, 23 d, 23 eindicating a synchronization mark are present on the photodetectors 31a, 31 b. These empty microcapsules have a high level of transmittance,both of which are detected by the photodetector 31. The capsules aredetected as synchronization marks. Therefore, the microcapsule 9 dfollowing these capsules is recognized as containing (n+3)^(th) DNA froma correspondence table. Therefore, it is possible to prevent ejection ofDNA having an erroneous number due to displacement of a microcapsule. Asynchronization mark is composed of 2, 3, or 4 empty capsules. One setcan contain 2-bit data. A synchronization capsule is used to match DNAitself to its DNA number, so that the matched DNA can be ejected. If DNAhaving a specific number is not ejected as in step 68 p of FIG. 15, lackinformation is recorded in the data region of FIG. 5. As shown in FIG.12, for example, a plurality of (n+1)^(th) DNA spots are formed as DNAspots 3 a, 3 b, 3 c. Therefore, a lack of DNA spot does not cause aproblem. In (7), the synchronization capsules 23 d, 23 e reach the tipportion. These capsules do not contain DNA and are unnecessary.Therefore, a removal signal is applied in (8), the capsules are deviatedand removed by the unnecessary liquid removing section 32 so that thecapsules do not reach the substrate 1. The removal circuit can preventunnecessary substances from being attached to the substrate 1.

[0500] A light detection signal, an eject signal, a removal signal andan arrangement of DNA spots will be described with reference to FIG. 10.Initially, a system is operated in accordance with a shift clock in FIG.10(3). Initially, since a DNA capsule has a low level of lighttransmittance as shown in FIG. (1), the DNA capsule is detected insynchronization with an eject signal in (4). Synchronization capsulesare detected as shown in (2) since the two photodetectors 31 a, 31 b areboth turned ON. As shown in (4), an eject signal is generated both for amicrocapsule containing DNA and a synchronization capsule containing noDNA. However, a removal signal of (5) is generated in synchronizationwith an eject signal following a detection signal of (2) so that allsynchronization capsules are removed. In the present invention, in orderto specify the DNA number of each DNA spot 2, positional data, such asaddress or the like, is buried as the intervals between DNA spots asshown in (11). When positional data is 12 bits in length, the positionaldata is divided into 00, 01, 10, 00, and 01 as shown in (10), where 00corresponds to a mark interval of 3 clocks and 01, 10 and 11 correspondsto 4t, 5t and 6t, respectively. Thus, interval modulation is performed.Further, there is a synchronization mark 37 having an interval of lot.With this method, positional information can be buried when DNA spotsare formed. Since the address of each DNA spot is obtained, the DNAnumber of a first DNA spot for a synchronization mark is obtained fromDNA number positional information 20 shown in FIG. 6. In the presentinvention, therefore, the DNA numbers of all DNA spots 2 can beidentified. The sequence information of all DNA spots can be obtained byusing sequence information 21 for DNA numbers recorded in the substrate1 of FIG. 6. Since the address is obtained, absolute precision is notrequired when the position of a DNA spot is read out. Therefore, ahigh-precision XY scanner is not required and it is possible to prepareand read a DNA spot with a low-precision apparatus, thereby making itpossible to supply an inexpensive DNA testing apparatus. In the priorart, ultrahigh-precision fabrication and readout apparatuses arerequired in order to increase the density of DNA spots. In the presentinvention, high density can be achieved by a low-precision fabricationand readout apparatuses. Further, since the attribute data of DNA spotsare recorded on the same substrate 1 as shown in FIG. 6, the possibilityof incorrectly reading out a DNA attribute is advantageously eliminated.

[0501]FIG. 30 shows a sub-nozzle 116, a sub-eject section 114, and asub-solution supply section 115 in addition to the system of FIG. 9. Thesub-nozzle 116 is supplied with microcapsules, and a sub-solution fromthe sub-solution supply section 115.

[0502] Operations will be described from (1) to (6) in sequence. In (1),(2) and (3), a DNA capsule 9 a is transported, and in (4), is ejected.In (5), a large volume of sub-solution is released from the sub-solutionsupply section 115 and then removed by the removal section 32. In (6), aDNA microcapsule 9 b is transported. In this method, the inside of thenozzle is washed with the sub-solution, whereby the mixing of DNA can beprevented.

Example 3 Fabrication Example of Biomolecule Chip (3): Tube Method

[0503] Next, a specific method for fabricating a biomolecule chipaccording to the present invention and a configuration thereof will bedescribed where a fiber convergence system is described as an example.Note that although in Example 3 a fiber convergence type fabricationmethod is used as an example, a method for burying data (e.g., address,chip ID, and the like) by arrangement of biomolecule spots, which is afeature of the present invention, can be applied to other methods, suchas a PIN method, an ink jet method, a semiconductor masking method, andthe like.

[0504] In this method, initially, a probe 131 corresponding to aspecific DNA, RNA and protein is injected together with a gel solutioninto a hollow thread tube 130 from a container 132 containing the probe131 in the gel form. Different probes 131 a, 131 b, 131 a, 131 d, etc.are injected into respective tubes 130 a, 130 b, 130 c, 131 c, 130 d,etc., which are then bundled in an X direction, i.e., horizontally, toform a sheet 133 as shown in FIG. 33(b). Further, the bundled sheets 133a, 133 b are piled so that the tubes 130 are arranged in a matrix toform a block 137 as shown in FIG. 33(c). The tubes may be arranged in acircle to form a column-like block.

[0505] In one embodiment of the present invention, a mark tube 134 for amark indicating an address or data is placed in the block. Note that ina second method, a mark tube 136 is placed in the block, which comprisesa probe solution 135 or a tube 130 in which a material for reflecting,absorbing, or emitting fluorescence having a specific wavelength iscontained. The mark tube 136 will be described in detail below. AlthoughFIG. 33(c) shows a 10×10 matrix, the actual matrix has a side of severalhundreds to several thousands of tubes.

[0506] The block 137 is sliced in a Z direction, so that a chip 138 iscompleted. The chip 138 is fixed on a fix plate 139. The fix plate 139is used to fix a chip and may comprise a container for holding aspecimen, and is shipped in this form. The fix plate 139 is used withoutmodification to perform testing. On the fix plate, a fix plate ID 140,which varies depending on corresponding attributes of probes, isrecorded in the form of a bar code, characters, or a bit pattern. A chipID for managing a process control or the attribute data of a chip isrecorded in the first sheet 133 a by a method for burying data accordingto the present invention. This attribute data can be used to identifychips having different probe sequences. Therefore, by checking, it ispossible to detect when an incorrect fix plate ID 140 is provided to achip 138.

[0507] (Method for Burying Data)

[0508] A spot of each probe is placed on the chip 138. Data is buried inan arrangement of spots. A spot containing the probe 131 for detectingDNA or protein is herein referred to as a DNA spot 2. Such a spot mayalso be called biomolecule spot. Now, a method for burying data will bedescribed. Specifically, as shown in FIG. 35(3), for example, 10biomolecule spots 141 e to 141 p are aligned in an x direction. Two markspots 142 a, 142 b are placed at the left end and three mark spots 142c, 142 d, 142 e are placed at the right end. Firstly, the case where themark spots include no biomolecule will be described. The case where themark spots include a biomolecule(s) will be described later.

[0509] A mark spot has an optical property different from a biomoleculespot 141 in terms of specific wavelength. Specifically, a mark spot hasa reflectance or absorbance with respect to a specific wavelength, orthe presence or absence of fluorescence or the intensity of fluorescencewith respect to a specific wavelength, different from a biomoleculespot. Therefore, a mark spot can be clearly distinguished from thebiomolecule spot 141. For example, when there is a difference inreflection or absorption with respect to excited light or irradiation,the mark spot can be optically clearly distinguished from thebiomolecule spot as indicated by hatched lines in FIG. 35(3). The sameeffect can also be obtained when the wavelength of fluorescence of themark spot 142 with respect to excited light is different from thewavelength of fluorescence of the biomolecule spot 141. The intensity ofreflected light or fluorescence obtained by irradiating the mark spotwith light having a specific wavelength is illustrated in FIG. 35(4). Agroup of the mark spots 142 in (3) are collectively calledidentification mark 143. 2-bit codes, “10”, “11”, and the like areassigned to respective identification marks 143 e, 143 f. FIG. 35(2)shows a general view including the identification marks 143 e, 143 fwhere part of biomolecule spots 141 between identification marks areomitted. This figure shows 7 identification marks 143 a to 143 g, towhich codes 00, 10, 11, 01, 10, 11, and 00 are assigned, respectively.When the identification marks 143 a, 143 g containing 4 consecutive markspots 142 are used as synchronization marks 144 a, 144 b, the fiveidentification marks 143 between the synchronization marks 144 can beused to bury 10-bit data, i.e., 10, 11, 01, 10, and 11.

[0510] By reading these marks with a scanning beam or a CCD in a testapparatus, the 10-bit data is read from this region. If these 10 bitsare used as, for example, address data, the address of this region,“1011011011”, can be obtained only by reading the 10 bits. Thus, a thirdbiomolecule spot 141 x to the right of the identification mark 143 c is23^(rd) biomolecule spot in address “1011011011”. Therefore, theidentification number 145 of a biomolecule spot can be identified as“101101011-23”. Therefore, all biomolecule spots 141 on a chip can beindividually identified without counting spots from an end of a matrix.Thus, a conventional method for identifying a spot by counting spotsfrom an end of a matrix to the x, y coordinates of the matrixcorresponding to that spot, is made unnecessary.

[0511] By reading out the attribute information of a biomolecule spot141 corresponding to the identification number 145 from an attributetable 146 in FIG. 40, various tests and diagnoses can be made possible.The attribute information contained in the attribute table 146 of FIG.40 includes the sequence or genetic information, or marker informationof a specific disease, of a biomolecule having this identificationnumber, or DNA, RNA, or other substances hybridizable to thisbiomolecule probe, and the like.

[0512] In an actual fabrication method, for example, a tube pilingmethod, errors in piling are accumulated, so that it is less likely thatthe x and y coordinate axes of a matrix can be precisely formed. In thiscase, therefore, the identification number of each biomolecule spotidentified from such x and y coordinates is highly likely to match thecorrect identification number. An incorrect identification number leadsto an incorrect test result. In the case of a DNA test or the like, whenan incorrect test result is used for diagnosis of a patient, falsediagnosis occurs frequently, potentially causing a serious problem.

[0513] In contrast, the present invention has an advantageous effectthat the identification number of a biomolecule 141 can be preciselyidentified by reading locally the vicinity of the biomolecule 141 evenif biomolecule spots are not arranged in a precise matrix. Biomoleculechip fabrication methods other than a semiconductor process can be usedto fabricate a large number of chips containing biomolecule spots. Evenin the case of a perfect matrix arrangement obtained by a semiconductorprocess, as the number of spots is increased, error occurs in countingspots on a test apparatus, potentially resulting in an incorrectidentification number. In the present invention, it is not necessary tocount spots with respect to x and y from an end of a biomolecule chip,and therefore, counting error does not occur. Moreover, theidentification number of each biomolecule spot can be obtained byreading only the vicinity of the biomolecule spot, whereby theidentification number of a desired biomolecule spot can be identified ina short time.

[0514] Specific procedures are as follows. For example, it is assumedthat DNA, RNA, or the like with a label emitting fluorescence with awavelength of λ2 has been hybridized to a biomolecule spot 141 x. Whenthe biomolecule spot 141 x is irradiated with excited light having awavelength of λ1, the biomolecule spot 141 x emitting fluorescence witha wavelength of λ2 can be observed. According to the data burying methodof the present invention, the identification number of the biomoleculespot 141 x is obtained and the sequence of the DNA or the like can beobtained from an attribute table, thereby making it possible to analyzeor test specimens.

Example 4 Test using Biomolecule Chip

[0515] (Test Procedures)

[0516] Procedures for test or diagnosis will be described with referenceto a flow chart shown in FIG. 41. Initially, in step 148 a, a specimenwith a fluorescent label is provided and hybridized to a surface of abiomolecule chip 138 fabricated by a chip fabrication process, such as atube method, a semiconductor process method, an ink jet method, a PINmethod, or the like. Unhybridized specimens, which are unnecessary, areremoved in step 148 b. This chip is loaded into a laser scanning typetest apparatus or a CCD readout type test apparatus shown in FIG. 14described later. In step 148 c, chip ID written in the first line of thechip 138 or/and a fix plate ID 140 on the fix plate 139 of FIG. 33 isread out by a light beam, CCD, or the like, so as to check the chip IDor the fix plate ID against a predetermined one. Next, these IDs arechecked against a predetermined ID list. If a result of theabove-described check is incorrect, the process is stopped. If theresult of the check is correct, an attribute table 146 (see FIG. 40)corresponding to the chip ID is obtained via a network 150, such as theInternet, LAN, or the like, and is temporarily stored in a memory 151 ofa test apparatus 149.

[0517] The process goes to a test mode. In step 148 d, m is set to be 0.In step 148 e, m is increased by one. In step 148 f, a surface of thechip is irradiated with excited light having a first wavelength of λ1.While scanning the chip using a laser or a CCD, a wavelength separationfilter, such as mirrors 65, 66 in FIG. 14, is used to search for m^(th)biomolecule spot emitting fluorescence with a specific wavelength. Thesearch is continued until the spot is found in step 148 g. When them^(th) biomolecule spot is found, the chip is irradiated with excitedlight or reference light in step 148 h. An optical property of a markspot 142, such as reflectance or the like, with respect to thewavelength of excited light is set to be different from that of abiomolecule spot 141. Therefore, as shown in FIG. 35(2), the mark spotcan be optically distinguished from the biomolecule spot using excitedlight or reference light. In this case, the same effect is obtained evenwhen the mark spot 142 emits fluorescence having a wavelength differentfrom that of the biomolecule spot 141. Therefore, the mark spot 142 canbe detected. In step 148 j, n is set to be 0. In step 148 k, n isincremented by 1, the code of n^(th) identification mark 143 isidentified. When the process is repeated until n reaches the last n instep 148 n, one data row is obtained. This data row contains an errorcorrection code 152 in order to improve the reliability of the data row.Therefore, the data row is subjected to error correction in step 148 p,and the data row having no error is obtained in step 148 q. In step 148r, by counting the number of spots from an identification mark 143closest to a subject biomolecule spot, the total number of biomoleculespots from a synchronization mark to the subject biomolecule spot 141(e.g., 141 x) as shown in FIG. 35(2) can be obtained. In step 148 s, theidentification number 145 of the m^(th) biomolecule spot is identifiedbased on the address and the number of counters. In this case, thewavelength of fluorescence can be specified from a filter setting, andtherefore, the label number of the fluorescence is identified.

[0518] In step 148 t, the attribute table 146 corresponding to chip IDis read out from the memory 151, and the sequence data of DNA or thelike having a specific identification number is retrieved as shown inFIG. 40. Therefore, the type of DNA, RNA, or a protein contained in aspecimen can be obtained. In step 148 u, this information and theidentification number are registered in to a test database 147 of thememory 151. In step 148 v, it is checked whether any other biomoleculespots emitting fluorescence remain unread. If there is an unread spot,the process returns to step 148 e and the biomolecule spot emittingfluorescence is located. If there is no unread spot, data of testdatabase 147 is sent to an analysis program 155 in step 148×. Instep 148y, an analyzed test or diagnosis result is output. Thus, the operationis completed.

[0519] As described above, according to the present invention, data,such as addresses, chip ID, or the like, is buried in the arrangement ofbiomolecule spots. Therefore, the identification number of a biomoleculespot of interest can be obtained from the arrangement of biomoleculespots or mark spots around the identification number of interest. Thisdata can contain chip ID and chip attribute data as well as addresses.In this case, all data required for testing or analysis is obtained froma chip itself. If chip ID obtained from a chip is compared with the fixplate ID 140 of the above-described fix plate, incorrect fix plate IDcan be checked in testing, thereby reducing the occurrence of erroneousdetection due to incorrect fix plate ID caused by a mistake in amanufacturing process. Further, it is possible to distribute abiomolecule chip alone without a fix plate 139, whereby chip cost can bereduced.

[0520] Note that, for the sake of simplicity, as shown in FIG. 35, theexample in which the biomolecule spot 141 containing biomolecules andthe mark spot 142 without a biomolecule, i.e., two types of spots, areused to bury data, such as addresses, has been first described. In thismethod, a mark spot is only added, and therefore, it is easy to managefabrication. On the other hand, the density of biomolecule spots isdisadvantageously reduced. For applications requiring a higherbiomolecule spot density, as shown in FIG. 34(a′), a mark solution 153having optical properties, such as a reflectance, absorbance, andrefractive index with respect to a specific wavelength, fluorescence,and the like, different from the solution 135 in (a) is introduced intoa tube. This tube is disposed as is a tube 130 a in (b). As shown in(d), a mark biomolecule spot 154 is formed on a chip. When it is notefficient to prepare two biomolecule solutions, i.e., one with a markand one without a mark, a mark may be attached to a tube 130 asrepresented by mark tubes 134, 136. In this case, although thesensitivity of such a mark is reduced, substantially the same effect asthat of a mark biomolecule spot 154 described in FIG. 36 is obtained.

[0521] This fabrication method can be applied to other applications. Inthe case of a PIN method, a mark material is added to a main solution 4or a sub-solution 8 as shown in FIG. 2 to prepare a mark solution 153.As shown in FIG. 38, biomolecules in a normal solution indicated by anunfilled circle and in a mark solution indicated by a filled circle arefixed to the substrate 1. Therefore, biomolecule spots 141 a to 141 iand the mark biomolecule spot 154 containing the mark solution 153 canbe formed on the substrate 1 as shown in FIG. 38. The description ofFIG. 38 is omitted because of substantially the same operation as inFIG. 3.

[0522] In the case of an ink jet method, a mark microcapsule 156containing biomolecules and a mark solution is loaded instead of thesynchronization capsules 23 d, 23 e shown in FIG. 11 so as to attach thecapsule 156 onto the substrate 1 as shown in FIG. 39(4), (5), (6), and(7). Thereby, the same arrangement of the biomolecule spot 141 and themark biomolecule spot 154 as in FIG. 38 can be obtained. Moreover, whena semiconductor mask is used, the same effect is obtained by piling amaterial for a mark on a mark biomolecule spot.

[0523] In the above-described three fabrication methods, the arrangementof the biomolecule spots 141 and the mark biomolecule spots 154 on thechip substrate is the same as in FIG. 36. The same effect as in the tubemethod can be obtained when the mark spot 142 is used instead of themark biomolecule spot 154 as shown in FIG. 35. In this case, a solutionor material containing only a mark solution without a biomolecule isimmobilized on a chip substrate in the three fabrication methods. Thefour exemplary fabrication methods have been described. The presentinvention can be applied to various biomolecule chip fabrication methodsother than the four examples.

[0524] Returning to FIG. 35, another data burying method will bedescribed. FIGS. 35(2) and (3) show that the mark spots 142 are arrangedso that data, such as addresses or the like, is buried, where the numberof consecutive mark spots is in the range of 1 to n. Hereinafter, adescription in parentheses corresponds to FIG. 41. FIG. 36(5) shows thatdata is buried by changing the interval between the mark spot 142 (markbiomolecule spot 154) depending on the data. Specifically, two markspots having an interval corresponding to 8 biomolecule spots is definedas a synchronization mark 157. The intervals between mark spots 142(mark biomolecule spots 154) from the synchronization mark 157 a to 157b are 4, 5, 6, 7 and 4. Therefore, data corresponding to 5 digits in theseptinary number system, i.e., 7 to the power of 5 pieces of data, canbe buried. This data can contain address data, error correction code,and chip attribute data. In this case, the mark spot can be easilydetected since the mark spot has the longest interval.

[0525]FIG. 35 (FIG. 36) (6) shows a method in which two consecutive markspots 142 (mark biomolecule spots 154) are arranged as a synchronizationmark 158. In this case, the intervals between mark spots 142 (markbiomolecule spots 154) from a synchronization mark 158 a to 158 b are 3,6, 4, 5, and 8. Therefore, 7 to the power of 5 pieces of data can beburied.

[0526]FIG. 37(a) shows an arrangement of long biomolecule spots 161 a,161 b and 161 c, and biomolecule spots 141 a to 141 k, which is obtainedby a tube method using a flat tube 160. When the elongated biomoleculespot 161 a is regarded as one mark spot, two contiguous elongatedbiomolecule spots 161 a, 161 b can be defined as a synchronization mark162. Similar to the synchronization mark 158 in FIG. 35(6), 7 data isread from an arrangement of 7 biomolecule spots 141 k, 141 j in FIG. 37.Thus, as shown in FIG. 37(b), “75456”, i.e., 5-digit data in theoctanary number system can be buried between the elongated biomoleculespot 161 b and the subsequent elongated biomolecule spot 161 (notshown).

[0527] In the present invention, a method for correcting an error indata using error correction codes is adopted. In the case of 10 bits, asindicated in a data structure diagram in FIG. 42, 10-bit original data159 (A₀ to A₉) is provided with 2-bit error correction codes 152 (C₀,C₁) produced from the original data 159 using Reed Solomon coding orturbo coding, thereby correcting an error. Therefore, the reliability ofburied data is increased, so that an error is unlikely to occur inimportant data, such as addresses. In FIG. 42, an error correction codeis used only in the horizontal direction. When a product code method inwhich an error correction code is additionally used in the verticaldirection, it takes a longer time to perform operations and obtainoriginal data. However, in this case, there liability of buried data isimproved.

Example 4 Detection Apparatus for Biomolecule Chip

[0528] In the above-described manner, a DNA chip or a DNA substrate, onwhich capture DNA is arranged, can be fabricated. This DNA substrate canbe used to test DNA or a protein.

[0529] DNA, such as cDNA or the like, is extracted from a DNA specimen,and is labeled with a fluorescence material 38 to prepare labeled DNA22. As shown in FIG. 13(1), the labeled DNA 22 is applied to a DNAsubstrate of the present invention. The DNA substrate is placed underspecific conditions, such as heating at several degrees Celsius and thelike, to carry out hybridization. As shown in FIG. 13(2), the labeledDNA 22 is coupled with capture DNA 3 a in the n^(th) DNA spot.

[0530] Now, a method for detecting this labeled DNA or a labeled proteinusing a DNA substrate of the present invention will be described. FIG.14 is a block diagram showing a detection apparatus 39 for detection.Firstly, the left half of the block diagram will be described. Lightemitted from an excitation light source 40, such as laser or the like,is converged by a mirror 41 having wavelength selectivity and a lens 42,and is focused on a substrate 1. Reflected light from the substrate 1reaches a detection section 43 via the mirror 41 and a polarizing mirror42. A focus error signal detection section 45 sends a focus error and atracking error to a focus control circuit 46 and a tracking controlcircuit 47, respectively. An actuator 48 drives and controls the lens 42in such a manner as to match the focus with tracking. A focus offsetsignal generation section 49 and a track offset signal generationsection 50 apply an offset to the focus and the tracking in order tooptimize a label detection signal. In the present invention, thearrangement of DNA spots 2 is intentionally modulated to includepositional information. A procedure for reproducing this data will bedescribed below.

[0531] A main signal is reproduced by a main signal reproduction section69. A positional information detection section 64 detects positionalinformation. A track number output section 52 and a DNA spot numberoutput section 51 send a currently scanned DNA spot number and tracknumber to a data processing section 55. Thereby, a DNA spot isidentified.

[0532] A signal from a data region 18 shown in FIG. 5 is reproduced todata by a demodulation section, such as EFM, PM, or the like, in themain signal reproduction section. The data is subjected to errorcorrection in an ECC decoder 53. DNA substrate attribute data shown inFIG. 6 is reproduced by a DNA substrate attribute data reading section54, and is sent to the data processing section 55. In the dataprocessing section 55, the capture DNA identification number 58 of acurrently scanned DNA spot 2 a is identified. A mirror 65 is used tosend fluorescence corresponding to the capture DNA identification number58 to a first label signal detection section 60. Therefore, the labelintensity data (fluorescence level, etc.) of a first identified DNAhaving a specific identification number corresponding to the capture DNA3 is output from the label signal output section.

[0533] A fluorescence dye 38 of the first labeled DNA 22 linked to theDNA spot 2 a is irradiated with excited light from a light source 40having a first wavelength λ0. After the emission of fluorescence isstarted and continued for the half life, the fluorescence comes to ahalf level. The half life is in the range of several nanoseconds toseveral tens of microseconds.

[0534]FIG. 17(1) shows the output power of excited light. FIG. 17(2)shows the intensity of fluorescence emitted from a fluorescent materialor a fluorescence dye by excited light. FIG. 17(2) shows that thefluorescence intensity comes to the half life at t=t6.

[0535] Now, a method for separating wavelengths will be described indetail with reference to FIG. 16. Of a plurality of incident light beamsλ0, λ1 and λ2, the excited light with wavelength λ0 having the highestintensity is reflected by the mirror 41 having an optical film 68 a witha film thickness of λ0/4. Fluorescence with wavelength λ1 from a firstlabel is reflected by the mirror 65 having an optical film 68 b with athickness of λ1/4, while fluorescence with wavelength λ2 transmits themirror 65. Thus, the three wavelengths are separated. The transmittanceof the separated wavelength is less than or equal to {fraction(1/1000)}, and therefore, the crosstalk between each wavelength issuppressed. Therefore, a weak fluorescence label level can be detected.A λ/4 filter for λ0 can be added to further improve the degree ofseparation, thereby making it possible to suppress the components of theexcited light source 40, and therefore, increasing the S/N ratio. Asshown in FIG. 18, an excited light beam 71 is made smaller than the DNAspot 2. For example, the size of the excited light beam 71 is as smallas several micrometers. In this case, the DNA spot 2 can be divided in ascanning direction, i.e., a direction of a scanning track 72. Theresultant portions are called cells 70 a, 70 b, 70 c, 70 d. Four piecesof data are obtained in the scanning direction, thereby making itpossible to measure the distribution of the amount of fluorescence withhigher precision. Cells 70 g, 70 h are measured as follows: a trackerror signal, which is V0 in the track offset signal generation section50, is intentionally generated; the track error signal is input to thetracking control circuit 47; an offset is generated in a trackdirection; and as indicated by a scanning track 72 a in FIG. 18, a trackis shifted so that the cells 70 g, 70 h are scanned while applyingexcited light to the cells 70 g, 70 h. When an inverse track errorsignal is input, cells 70 e, 70 f can be scanned. Thus, in the case ofFIG. 18, the DNA spot 2 is divided into 8 cells which can be scanned andirradiated with excited light.

[0536] Next, a detection procedure will be described with reference toFIG. 20. FIG. 20(1) shows that DNA spots 2 a to 2 i are arranged on aDNA substrate 1. In (2), first labeled DNA 22 a having a label with afirst fluorescence wavelength λ1 and second labeled DNA 22 b having alabel with a second fluorescence wavelength λ2 are introduced onto asubstrate to carry out hybridization. The first labeled DNA 22 a iscomplementarily coupled with DNA contained in DNA spots 2 b, 2 e, 2 h.The second labeled DNA 22 b is coupled with a DNA spot 2 h. In (3),drying is performed, and scanning is started using an excited lightsource 40 with a wavelength λ0. (4) shows an excited light detectionsignal for reflected light of the excited light. Fluorescence generatedby the excited light with the wavelength λ0 does not contain awavelength component of λ0, so that only a detection signal with λ0 isobtained. The surface of the substrate 1, such as glass or the like, hasa certain reflectance. Nevertheless, a reflection layer may be furtherformed on the surface of the substrate of FIG. 1 in order to increasethe signal level of the excited light detection signal. A detectionsignal as shown in (4) is obtained due to the difference in reflectancebetween the reflectance of a DNA spot 2 with respect to λ0 and thesurface of the substrate 1. As described concerning the procedure forDNA spot formation with reference to FIG. 10, positional data or thelike is buried by changing the pattern or arrangement of DNA on thesubstrate 1 of the present invention depending on specific data. Asshown in (4), the interval between detection signals varies. As aresult, signals 00, 01, 10, 00, 01, 01 can be reproduced as shown in(5). Based on these signals, positional data, i.e., address informationas shown in (6) can be reproduced. Therefore, for example, it can befound that a DNA mark 2 a is located in 260^(th) track and at 1128^(th)address. A detection apparatus obtains DNA substrate attribute data fromthe data region 18 of the substrate 1 as described with reference toFIG. 6. Specifically, for example, the start number of DNAidentification number in 260^(th) track in DNA number positionalinformation 20 is 243142. Therefore, DNA having identification number244270 can be identified. Further, when the user can obtain anencryption key 73, encrypted DNA sequence information for DNA number(=244270) in sequence information 21 by DNA number is decoded by acipher decoder 74. Thereby, the DNA spot 2 can be identified to theextent that the DNA spot 2 has a DNA sequence ATCTAGTA . . . Note thatwhen the user does not have the encryption key 73, DNA sequence is notdecoded. In this case, even if the fluorescence data of a DNA spot isobtained, the privacy of personal DNA information is protected. In apostscript data region 76 of FIG. 6, first label attribute data 77 andsecond label attribute data 78 of hybridized labeled DNA is additionallyrecorded, such as the excited light wavelengths 410 nm, 410 nm oflabels, fluorescence wavelengths 700 nm, 600 nm, half lives 100 ns, 100ns, or the like. Therefore, the operations of the detection apparatuscan be checked or set using this postscript data.

[0537] Returning to FIG. 20, a procedure for measuring the fluorescenceof a label generated by excited light will be described. Initially, asdescribed in FIG. 18, in the case of the scanning track 72, cells 70 a,70 b, 70 c, 70 d are scanned with excited beam 71. In the case of a DNAspot 2 b, fluorescence with a wavelength λ1 is generated, and isdetected by the first label signal detection section (FIG. 14). As aresult, a first label detection signal 85 a corresponding to the fourcells are detected as shown in (8). When a DNA spot 2 g is scanned,fluorescence with a wavelength λ2 is generated, and a second labeldetection signal 85 b is generated as shown in (9). When an offset isapplied in FIG. 18, i.e., in the case of the scanning track 72 a, alabel detection signal 85 c resulting from detection of fluorescenceonly from two cells is obtained as shown in (10).

[0538] In the present invention, when a higher detection sensitivity oflabeled DNA is required, the excited light source 40 is caused to emitintermittently. A shift amount in a linear direction or a rotationaldirection of the substrate is detected by a shift amount detector 86. Apulsed light emission signal 88 or a sub-pulsed light emission signal 87having reversed phase is generated by the pulsed light emission controlsection 87 depending on the shift amount. In first scanning, as shown in(11), when the pulsed light emission signal 88 is applied to the lightsource 40, pulsed light emission is performed. As a result, first andthird cells, i.e., cells 70 a, 70 c, generate fluorescence. In thismethod, fluorescence is detected when the light source 40 is in the OFFstate. Therefore, a considerably high SIN is obtained. For example, alabel detection signal 85 d is obtained as shown in (13). In this case,a light receiving portion of the first label detection section isslightly shifted, so that light receiving efficiency is improved. Insecond, i.e., even numbered, scanning, a sub-pulsed light emissionsignal having reversed phase as shown in (12) is input to the lightsource 40, and the same track 72 is scanned. Due to the reversed phasewith respect to the first scanning, second and fourth cells, i.e., cells70 b and 70 d (two clocks after) (FIG. 18) are irradiated with excitedlight. During the subsequent on clock, excited light is OFF. Therefore,fluorescence from the cell 70 b or 70 d can be detected withoutinterference by excited light. Thus, by scanning two times, thefluorescence levels of all cells can be advantageously detected withhigh sensitivity. A description will be given with reference to aflowchart of FIG. 31. In step 118 a, scanning is performed once so thatthe arrangement information of all DNA spots on the track is stored intoa memory (steps 118 b, 118 c). In this case, in step 118 d, if scanningis performed at a constant speed in the second time or thereafter, thepositions of the DNA spots can be reproduced by reading out from thememory (step 118 f).

[0539] A description will be given with reference to FIGS. 31 and 32. Instep 118 g, excited light is intermittently emitted at odd numberedclock times (FIG. 32(2)). Fluorescence is generated (FIG. 32(4)). Instep 118 h, fluorescence is detected based on a detection permittingsignal of FIG. 32(3) (FIG. 32(5)).

[0540] In third scanning, excited light is intermittently emitted ateven numbered clock times in step 118 j (FIG. 32(6)). In step 118 k,fluorescence is intermittently detected (FIG. 32(9)). Therefore, theinfluence of excited light is eliminated, whereby SN is improved.

[0541] Accordingly, in the present invention, high precision in thelinear direction is obtained even by pulsed light emission. No problemarises in precision in the track direction.

[0542] Next, a method for improving sensitivity while enhancingpositional resolution will be described. Referring to FIG. 19, thesubstrate 1 is moved so that the cell 70 b is moved in the order of (1),(2), (3), (4), (5), and (6). In order to measure the amount offluorescence from the substrate 1, a light detection section 90 has anarray structure 91 and perform switching in the order of (1′), (2′),(3′), (4′), (5′), and (6′), depending on the shift amount. Thereby, ahigh level of sensitivity is obtained while keeping a resolution. FIG.21 is a block diagram showing that switching is performed on the arrayby a switching section 92 based on a signal from the shift amountdetector 87 and a synchronization signal from the DNA spot 2; thefluorescence of the cell 70 b is tracked, and fluorescence data isaccumulated and output by an addition section 93. In this case, if theamount of shift from the center of a cell is within f×0.05 where frepresents the focal distance of the lens 42, the cell can be detectedby the array 91.

[0543] A label detection signal list 94 in the detection apparatus hasdata as shown in FIG. 22. This data is recorded into the data region 18of FIG. 5 with excited light. In this case, all data can be integratedwith a single substrate. Therefore, the possibility of obtainingincorrect data is eliminated, thereby avoiding accidents, such as falsediagnosis and the like.

[0544]FIG. 23 shows that a recording layer 95 is added to a substrate 1and a light source 40 and a lens 42 a are provided on the opposite sideof the substrate to the recording layer 95. Since data can be recordedin the recording layer 95, a large volume of data can be recorded. FIG.24 shows that two upper and two lower actuators 48, 48 a aremechanically coupled together. In this case, as shown in FIG. 25, sincethe position of each DNA spot 2 a can be defined with an address 96 inthe recording layer 95, the outer shape of the DNA spot 2 a can bespecified with a start address 97, an end address 98, innermostcircumferential track number 99, and an outermost circumferential tracknumber 100, thereby making it possible to access a DNA spot at highspeed. This correspondence list can be recorded in the recording layer95. Referring to FIG. 26, DNA spots 2 a, 2 b, 2 a are in the shape of arectangle, thereby making it possible to perform scanning tracking withhigher accuracy. FIGS. 27 and 28 shows DNA chips as shown in FIG. 5 butin the shape of a circle. In particular, the entire rear surface of theDNA chip of FIG. 28 can be used. Therefore, the DNA chip of FIG. 28 hasa large recording capacity and can store the entirety of a DNA sequence.The term DNA is herein used. Any biomolecule as defined herein (e.g., aprotein) may be used as a subject substance to be labeled. RNA may beused instead of DNA. Cells or a part of tissue may be used as long asthey can be arranged on a substrate.

[0545] In the embodiments, as a method for fabricating a DNA substrate,a PIN method and an ink jet method are employed to describe the examplesof the present invention. However, the present invention can also beapplied to a semiconductor process method. Referring to FIG. 29, in asemiconductor process method, probe DNA is arranged on a glasssubstrate. Referring to FIG. 29(2), lithography is performed as follows.A mask 120 is used to perform masking. Specific probe DNA is irradiatedto activate an elongation reaction probe DNA containing A (adenine) 123is formed as shown in FIG. 29(3). Thereafter, C (cytosine) 124 is formedas shown in FIG. 29(4) and (5). This elongation reaction is carried outfor A, C, G, and T, i.e., four times, to complete one layer. If theelongation reaction is carried out 4N times as shown in FIG. 29(6),probe DNAs having a length of N bases are formed. In the DNA chipfabrication of the semiconductor process method, the position of theopening of the masking is shifted as shown in FIG. 10(7) using thepresent invention. As shown in FIG. 29(1), a mask 121 a is shifted withrespect to the original mask 121 b in correspondence with specific data.Thereby, positional data can be buried and recorded in an arrangement ofDNA spots.

Example 6 Network Type Test Apparatus

[0546] An operation of a test system using a biomolecule chip accordingto the present invention will be described. FIG. 43 is a flowchartshowing the operation of the test system of the present invention. In abiomolecule extraction section 172, a biomolecule is extracted,purified, or grown from a sample 171 collected from a subject 170 toprepare a specimen 173. In a test section 175 of a main test system 174,this specimen 173 is loaded to a biomolecule chip 138, followed by areaction. A portion of molecules in the specimen 173 are hybridized withprobes in a specific biomolecule spot 141 as described above. Thisbiomolecule spot exhibits label information, such as fluorescence or thelike, and therefore, can be easily detected. On the other hand, a chipID 19 can be detected from the biomolecule chip 138. These test data areencrypted together with the chip ID 19 (substrate ID 19 is also referredto as chip ID 19), and the encrypted data is sent via a communicationsection 176 and then through the Internet 177 or a communication circuitto a communication section 179 of a sub-test system 178, such as a testcenter or the like. Thereafter, the data is sent to an analysis section181 of an analysis system 180. In the analysis section 181, theattribute data of each biomolecule spot of a corresponding chip ID canbe obtained from an identification number-attribute database 184. Fromthe obtained attribute data and label number, the state of the specimen173, such as a gene, a protein or the like, can be identified.

[0547] An analysis result in the case of genetic information is shown inFIG. 45. Firstly, a gene number 183 corresponding to a gene sequence isshown. Gene attribute data indicating a gene attribute 184 of a genecorresponding to the number contains the sequence of the gene; a markerfor a disease, a character, or the like; and the like. Since this typeof test is used in a test of a specific disease or a test of a specificmolecule, the main test system 174 outputs a request, such as,specifically for example, data “Please output information relating to adisease a”. As shown in a selective output 185 of FIG. 45, onlyinformation relating to a request output 186 is selected by a selectionsection 182, and is encrypted by the output section 183 and sent via thecommunication section 179 and the Internet 187 to the main test system174.

[0548] In a gene test, data which is not originally intended is obtainedin the course of testing and analysis. For example, when geneticinformation on a specific cancer is required, if unintended geneticinformation, such as other diseases or characters (e.g., an intractableand unavoidable disease (juvenile Alzheimer's disease, etc.), acatastrophic character, etc.), is output, the interest of a subject islikely to be damaged. If this type of information is unintentionallyleaked, a privacy problem occurs. According to the present invention,the selection section 182 filters out information unrelated to a requestoutput or raw genetic information, thereby making it possible to preventunnecessary information from being output.

[0549] The result of a test corresponding to a chip ID, which isrequested to the main test system 174, is received by the diagnosissystem 187 and processed by a diagnosis section 188. The chip ID-subjectcorrespondence database 191 can be used to identify the subject 170 froma chip ID 19. All chips have a unique chip ID. Therefore, the subjectcorresponding to each chip can be identified. This data is not sent toany sub-test system. Therefore, patient data is prevented from beingleaked to a test laboratory or the outside of a hospital. The testsystem can know the relationship between a subject and a chip ID, butdoes not have the attribute data of each biomolecule spot of the chipID. Unless the attribute data is obtained from the sub-test system,whole genetic information cannot be obtained. In other words, the maintest system 174 and the sub-test system 178 each have incompletecomplementary information, thereby maintaining security. Thus, thesecurity of the genetic information of a subject can be protected.

[0550] In this case, each chip ID is different from the others and isprovided with a randomized number. Therefore, even if all the attributeinformation of a chip having a certain chip ID number (e.g., theattribute data of a biomolecule corresponding to the identificationnumber in each biomolecule spot) is made public, the data of any otherchip ID cannot be identified, since there is no correlation between thespecific chip ID and the other chip IDs. The security of the wholesystem can be protected as long as the secrecy of the sub-test systemcan be maintained. When the secrecy of the main test system ismaintained, no information connecting a chip to a person is obtainedeven if a chip and a personal ID are obtained by a third party. In thiscase, security is further improved.

[0551] The diagnosis section 188 outputs a result of diagnosis based onhistoric data of a subject (a disease, etc.) and a test result obtainedfrom the sub-test system. A diagnosis result output section 192externally outputs the diagnosis result. A treatment policy productionsection 189 produces a plurality of treatment policies based on thediagnosis result, assigns priorities to the treatment policies, andoutputs the treatment policies through the output section 190.

[0552] (Utilization of Genetic Information Other than Diseases)

[0553] In the above-described examples, information relating to aspecific disease is specified as request information and is sent out asa request output 186. Recently, it has been revealed that apsychological attribute, such as a character or the like, of a subjectcan be obtained from genetic information. For example, a person havingthe third exon of the dopamine D4 receptor on the 11^(th) chromosome hasa character of challenge. Thus, now and thereafter, attributeinformation, such as a personal character, will be clarified fromgenetic information one after another. Considering this point, attributedata indicating a psychological feature, such as a character, of asubject is added to the disease data in the request output 186 of FIG.43. In this case, information on the character, aptitude, or the like ofa subject 170 is sent from a sub-test system to the diagnosis system187. The priorities of the treatment policy options of the treatmentpolicy production section 189 are changed depending on the attribute andaptitude data of the subject. For example, for a subject who prefers ahigh risk and a high result, the priority of a treatment option whichprovides a high result at a high risk is increased. For a subject whoprefers a moderate result at a low risk, the priority of a therapeuticagent, which is safe but whose effect is not high, is increased. Withthis method, a diagnosis system for providing a treatment policysuitable for the character or aptitude of a subject can be achieved.

Example 7 Stand-alone Test Apparatus

[0554] The operation (security, etc.) of the present invention has beendescribed using the exemplary network type test apparatus of FIG. 43.The present invention can be applied to a stand-alone type test system193 as shown in FIG. 44.

[0555] The network type test system of FIG. 43 comprises two systems,i.e., a main test system and a sub-test system. The latter isadministered by a neutral entity, such as a test center, and can enhancesecrecy to maintain the security of the whole system. In contrast, thestand-alone type test system of FIG. 44 includes a black box section 194having a high level of secrecy instead of the sub-test system 178. Theblack box section 194 leaks no internal information other thaninformation required to be output to the outside. Only required data isoutput from an input/output section 195. The security of information ismaintained by the black box section 194.

[0556] Most portions of the stand-alone type test apparatus have thesame operation as in FIG. 43. Only different points than those in FIG.43 will be described below. Initially, in a test section 175, encrypteddata, such as encrypted biomolecule spot-attribute data 146 encryptedusing public key encryption function or the like, is reproduced by achip 138 and is sent to a black box section 194. This encrypted data isdecoded to plain text data by a cipher decoding section 197 within theblack box section 194. This plain text data contains attributeinformation relating to each biomolecule spot on a biomolecule chip. Theattribute information is added to a biomolecule spot identificationnumber-attribute database 184.

[0557] In the case of FIG. 43, the main test system accesses via anetwork to the database 184 in a sub-test system, such as a test centeror the like and obtains data. Therefore, such a sub-test system, such asa test center or the like, needs to obtain the latest data of all chipsproduced all over the world and update the data as occasion demands. Themain test system cannot obtain a test result unless a network isavailable. However, in the method of FIG. 44, even if a chip is recentlyproduced, the attribute data 146 is present in the biomolecule chip, andthis attribute information is automatically recorded into theidentification number-attribute data correspondence database 184, whichis thus updated, every time a chip is loaded in a test system.Therefore, the stand-alone type test system does not have to beconnected to a network. Moreover, a memory of the test system storesdata corresponding to only one chip. Therefore, memory capacity can besignificantly reduced. In the case of this method, a mobile type testapparatus can be used. Similar to FIG. 43, in this method, onlyinformation relating to an output requested from the main test system isselected by a selection section 182, and is sent from the black boxsection 194 to a diagnosis system 187 in the main test system 174.

[0558] Note that if the black box section 194 is produced in such amanner that, for example, the black box section 194 is incorporated intoa chip of LSI and its external terminals are limited to the input/outputsection 195 and the cipher decoding section 197, no internal data can beexternally read out. Therefore, security is protected. As describedabove, with a biomolecule chip containing encrypted data of the presentinvention and a stand-alone type test system of the present invention,required testing or diagnosis can be carried out without a network orexternally input data while protecting the information security of asubject.

[0559] Note that although the above-described example is such that theattribute information of a biomolecule chip is buried in the arrangementdata of biomolecule spots, such information may be optically recordedwith pit marks or the like on a substrate integrated with a chip asshown in FIG. 5. Alternatively, as shown in FIG. 46, a biomolecule chip138, an IC chip 198 having a non-volatile memory 201, and an electrode199 are provided on a substrate 200, the attribute information may berecorded in the non-volatile memory 201 of the IC chip 198. Theattribute information may be optically read out in the test system, ormay be electrically read out from the electrode 199 or the like.

[0560] All of the publications, patents, and patent literature citedherein are each incorporated herein by specific reference. The presentinvention has been described with reference to various particular andpreferable embodiments and techniques. However, it should be understoodthat various modifications and variations can be made without departingfrom the spirit and scope of the present invention.

[0561] Note that in the description of the embodiments, the arrangementof biomolecule spots is changed in the same direction as a singlespecific arrangement direction of biomolecule spots. However, othermethods can be easily implemented, though their descriptions areomitted. First of all, the size of a biomolecule spot may be changed.Specifically, data “01” is assigned to a biomolecule spot having a smallsize; “10” is assigned to a biomolecule spot having a middle size; and“11” is assigned to a large size. Thus, three-valued data can be buriedin one biomolecule spot.

[0562] Alternatively, the position of a biomolecule spot may beintentionally shifted from a reference position in a directionperpendicular to a specific arrangement direction of biomolecule spots.Specifically, data “01” is assigned to a biomolecule spot shifted by+20% with reference to the reference position; “10” is assigned to abiomolecule spot shifted by 0%, i.e., not shifted; and “11” is assignedto a biomolecule spot shifted by −20%. In this case, three-valued datacan be buried in one biomolecule spot. If the number of the shiftamounts or resolutions is increased, multivalued data, such asfive-valued data, seven-valued data, or the like, can be buried.

[0563] Alternatively, the size of a biomolecule spot may be changed in adirection perpendicular to a specific arrangement direction without theposition of the biomolecule spot. For example, data “0” is assigned toan elliptic biomolecule spot having a major axis in the verticaldirection, and data “1” is assigned to a circular biomolecule spot,thereby making it possible to bury two-valued data. Alternatively, thesize of a biomolecule spot may be changed in the same direction as thearrangement direction.

[0564] If a plurality of methods of the above-described burying methodsare simultaneously used, the amount of buried data can be furtherincreased.

INDUSTRIAL APPLICABILITY

[0565] As described above, in the present invention, the position orpattern itself of a biomolecule (e.g., DNA, RNA, a protein, a low weightmolecule, etc.) is changed to bury the positional information of thebiomolecule. Therefore, no extra process is required and conventionalhigh-precision positioning is no longer required. This method is moreeffective when the number of types of biomolecule is large and thedensity of biomolecules is required. Further, a test apparatus can readout the positional information of a DNA spot using an excited lightsource, and therefore, biomolecule spots may be only relativelypositioned. No conventional high-precision apparatus for absolutelypositioning biomolecule spots is required. Thus, a test apparatus can beobtained by only a simple configuration. Furthermore, data is recordedon a substrate, and the data is read out using excited light. Therefore,the attribute data of a biomolecule spot can be read out from the samesubstrate without increasing the number of components, whereby datamatching error is eliminated. The above-described advantageous effectsaccelerates widespread use of a biological test apparatus and diagnosisapparatus.

1 4 1 12 DNA Artificial Sequence unsure 10..12 Description of ArtificialSequence an oligonucleotide chemically synthesized by a method known tothose skilled in the art 1 atgctgatannn 12 2 9 DNA Artificial SequenceDescription of Artificial Sequence an oligonucleotide chemicallysynthesized by a method known to those skilled in the art 2 atgctgata 93 10 DNA Unknown unsure 8..10 Description of Unknown Sequence anoligonucleotide collected from an organism or chemically synthesized bya method known to those skilled in the art 3 tacgactnnn 10 4 10 DNAArtificial Sequence unsure 5..10 Description of Artificial Sequence anoligonucleotide chemically synthesized by a method known to thoseskilled in the art 4 atgannnnnn 10

1. A method for fabricating a biomolecule substrate, comprising the steps of: 1) providing a set of biomolecules and a substrate; 2) enclosing the set of biomolecules into microcapsules on the biomolecule-type-by-biomolecule-type basis; and 3) spraying the biomolecule microcapsules onto the substrate.
 2. A method according to claim 1, further comprising the step of washing the biomolecule microcapsules after the enclosing step.
 3. A method according to claim 1, wherein the spraying step is performed by an ink jet method.
 4. A method according to claim 3, wherein the ink jet method is performed by a Bubble Jets method.
 5. A method according to claim 1, further comprising the step of setting the temperature of a solution used in the spraying step to be higher than the melting point of a shell of the biomolecule microcapsulate.
 6. A method according to claim 1, wherein the microcapsules of the set of biomolecules of different types are disposed at different positions.
 7. A method according to claim 1, wherein the spraying step is performed by a PIN method.
 8. A method according to claim 1, wherein the biomolecule contains at least one of DNA, RNA and a peptide.
 9. A method according to claim 1, wherein the biomolecule is DNA.
 10. A method according to claim 1, wherein the biomolecule is cDNA or genomic DNA.
 11. A method according to claim 1, further comprising the step of perform labeling specific to each microcapsule.
 12. A biomolecule chip, comprising: a substrate; and biomolecules and chip attribute data arranged on the substrate, wherein the chip attribute data is arranged in the same region as that of the biomolecules.
 13. A biomolecule chip according to claim 12, wherein the chip attribute data contains information relating to chip ID and the substrate.
 14. A biomolecule chip according to claim 12, further comprising a recording region, wherein the recording region is placed on the same substrate as that of the biomolecule and the chip attribute data, and at least one of subject data and measurement data is recorded in the recording region.
 15. A biomolecule chip according to claim 12, wherein the chip attribute data is recorded in such a manner as to be read out by the same means as that for detecting the biomolecule.
 16. A biomolecule chip according to claim 12, wherein a specific mark is attached to the substrate.
 17. A biomolecule chip according to claim 12, wherein a specific mark is arranged based on the chip attribute data.
 18. A biomolecule chip according to claim 12, wherein the chip attribute data contains the biomolecule attribute data.
 19. A biomolecule chip according to claim 12, wherein information relating to an address of the biomolecule is further recorded.
 20. A biomolecule chip according to claim 19, wherein the address is a tracking address.
 21. A biomolecule chip according to claim 12, wherein the chip attribute data is encrypted.
 22. A biomolecule chip according to claim 12, wherein data relating to a label used to detect the biomolecule is recorded.
 23. A biomolecule chip according to claim 22, wherein the data relating to the label contains at least one of the wavelength of excited light and the wavelength of fluorescence.
 24. A biomolecule chip according to claim 12, wherein the biomolecule contains at least one of DNA, RNA and a peptide.
 25. A biomolecule chip according to claim 12, wherein the biomolecule is DNA.
 26. A biomolecule chip according to claim 12, wherein the biomolecule is cDNA or genomic DNA.
 27. A biomolecule chip, comprising: 1) a substrate; and 2) biomolecules arranged on the substrate, wherein spots of the biomolecules are spaced by at least one non-equal interval, an address of the biomolecule spot can be identified from the non-equal interval.
 28. A biomolecule chip according to claim 27, wherein the non-equal interval is modulated.
 29. A biomolecule chip according to claim 27, wherein the non-equal interval is present in at least two directions.
 30. A biomolecule chip, comprising: 1) a substrate; and 2) biomolecules arranged on the substrate, wherein the biomolecules include a distinguishable first biomolecule and a distinguishable second biomolecule, an address of the biomolecule can be identified based on an arrangement of spots of the first biomolecules and spots of the second biomolecule.
 31. A biomolecule chip according to claim 27 or 30, wherein a label distinguishable from the biomolecule is placed between the biomolecule spots.
 32. A biomolecule chip according to claim 31, wherein the distinguishable label can be detected by detection means.
 33. A biomolecule chip according to claim 31, wherein the label is arranged in a horizontal direction and a vertical direction on the substrate.
 34. A biomolecule chip according to claim 27 or 30, wherein a synchronization mark is arranged.
 35. A biomolecule chip according to claim 27 or 30, wherein the biomolecule contains at least one of DNA, RNA and a peptide.
 36. A biomolecule chip according to claim 27 or 30, wherein the biomolecule is DNA.
 37. A biomolecule chip according to claim 27 or 30, wherein the biomolecule is cDNA or genomic DNA.
 38. A biomolecule chip, comprising: 1) a substrate; and 2) biomolecules arranged on the substrate, wherein spots storing attribute data are arranged on a side of the substrate opposite to a side on which spots of the biomolecules are arranged.
 39. A biomolecule chip according to claim 38, wherein the attribute data is address information.
 40. A biomolecule chip, comprising: 1) a substrate; 2) biomolecules arranged on the substrate; and 3) a data recording region.
 41. A biomolecule chip according to claim 40, wherein the data recording region is placed on the side opposite to the side on which the biomolecules are arranged.
 42. A method for detecting a label of a biomolecule chip, comprising the steps of: 1) providing a biomolecule chip on which at least one labeled biomolecule is arranged; 2) switching detection elements sequentially for detecting the biomolecules on the biomolecule chip; and 3) identifying a signal detected by the detection element.
 43. A method according to claim 42, further comprising: 4) adding up each detected signal.
 44. A method according to claim 42, wherein the signal is separated by a wavelength separation mirror.
 45. A method according to claim 42, wherein the biomolecule substrate further contains a synchronization mark, and the label is identified based on the synchronization mark.
 46. A method according to claim 42, wherein the biomolecule substrate contains address information on a rear side of the biomolecule, and the label is identified based on the address information.
 47. A method for detecting information on an organism, comprising the steps of: 1) providing a biomolecule sample from the organism; 2) providing a biomolecule chip according to claim 27 or 30; 3) contacting the biomolecule sample to the biomolecule chip, and placing the biomolecule chip under conditions which causes an interaction between the biomolecule sample and a biomolecule placed on the biomolecule; and 4) detecting a signal caused by the biomolecule and a signal caused by the interaction, wherein the signal is an indicator for at least one information parameter of the organism, and the signal is related to an address assigned to the non-equal interval or the spot arrangement.
 48. A method according to claim 47, wherein the biomolecule sample contains nucleic acid, and the biomolecule placed on the biomolecule chip is nucleic acid.
 49. A method according to claim 47, wherein the sample contains a protein and the biomolecule placed on the biomolecule chip is an antibody, or the sample contains an antibody and the biomolecule placed on the biomolecule chip is a protein.
 50. A method according to claim 47, further comprising labeling the biomolecule sample with a label molecule.
 51. A method according to claim 50, wherein the label molecule can be distinguished from the biomolecule placed on the biomolecule chip.
 52. A method according to claim 50, wherein the label molecule contains a fluorescent molecule, a photophorescent molecule, a chemoluminescent molecule, or a radioactive isotope.
 53. A method according to claim 47, wherein the signal detecting step is performed at a site different from where the interaction occurs.
 54. A method according to claim 47, wherein the signal detecting step is performed at the same site as where the interaction occurs.
 55. A method according to claim 47, further comprising encrypting the signal.
 56. A method according to claim 47, further comprising subjecting the signal to filtering so as to extract only signal relating to required information.
 57. A method for diagnosing a subject, comprising the steps of: 1) providing a sample from the subject; 2) providing a biomolecule chip according to claim 27 or 30; 3) contacting the biomolecule sample to the biomolecule chip, and placing the biomolecule chip under conditions which cause an interaction between the biomolecule sample and a biomolecule placed on the biomolecule; 4) detecting a signal caused by the biomolecule and a signal caused by the interaction, wherein the signal is at least one diagnostic indicator for the subject, and the signal is related to an address assigned to the non-equal interval or the spot arrangement; and 5) determining the diagnostic indicator from the signal.
 58. A method according to claim 57, wherein the sample is nucleic acid, and the biomolecule placed on the biomolecule chip is nucleic acid.
 59. A method according to claim 57, wherein the sample contains a protein and the biomolecule placed on the biomolecule chip is an antibody, or the sample contains an antibody and the biomolecule placed on the biomolecule chip is a protein.
 60. A method according to claim 57, further comprising labeling the sample with a label molecule.
 61. A method according to claim 60, wherein the label molecule can be distinguished from the biomolecule placed on the biomolecule chip.
 62. A method according to claim 60, wherein the label molecule is a fluorescence molecule, a photophorescent molecule, a chemoluminescent molecule, or a radioactive isotope.
 63. A method according to claim 57, wherein the diagnostic indicator is an indicator for a disease or a disorder.
 64. A method according to claim 57, wherein the diagnostic indicator is based on single nucleotide polymorphism (SNP).
 65. A method according to claim 57, wherein the diagnostic indicator is based on a genetic disease.
 66. A method according to claim 57, wherein the diagnostic indicator is based on the expression level of a protein.
 67. A method according to claim 57, wherein the diagnostic indicator is based on a test result of a biochemical test.
 68. A method according to claim 57, wherein the determining step is performed at a site different from where the interaction occurs.
 69. A method according to claim 57, wherein the signal detecting step is performed at the same site as where the interaction occurs.
 70. A method according to claim 57, further comprising encrypting the signal.
 71. A method according to claim 57, further comprising subjecting the signal to filtering so as to extract only signal relating to required information.
 72. A method according to claim 57, wherein in the detecting step biomolecule attribute data is hidden, and in the determining step personal information data is hidden.
 73. A test apparatus for information on an organism, comprising: 1) a biomolecule chip according to claim 27 or 30; 2) a sample applying section in fluid communication with the biomolecule chip; 3) a reaction control section for controlling a contact and an interaction between the biomolecule placed on the biomolecule and a biomolecule sample applied from the sample applying section; and 4) a detection section for detecting a signal caused by the interaction, wherein the signal is an indicator for at least one information parameter of the organism, and the signal is related to an address assigned to the non-equal interval or the spot arrangement.
 74. A test apparatus according to claim 73, further comprising a section for receiving and sending the signal.
 75. A test apparatus according to claim 73, further comprising a region for recording the signal.
 76. A diagnosis apparatus for a subject, comprising: 1) a biomolecule chip according to claim 27 or 30; 2) a sample applying section in fluid communication with the biomolecule chip; 3) a reaction control section for controlling a contact and an interaction between the biomolecule placed on the biomolecule and a biomolecule sample applied from the sample applying section; 4) a detection section for detecting a signal caused by the biomolecule and a signal caused by the interaction, wherein the signal is an indicator for at least one information parameter of the organism, and the signal is related to an address assigned to the non-equal interval or the spot arrangement; and 5) determining the diagnostic indicator from the signal.
 77. A diagnosis apparatus according to claim 76, further comprising a section for receiving and sending the signal.
 78. A diagnosis apparatus according to claim 76, further comprising a region for recording the signal.
 79. A biological test system, comprising: A) a main sub system, comprising: 1) a biomolecule chip according to claim 27 or 30; 2) a sample applying section in fluid communication with the biomolecule chip; 3) a reaction control section for controlling a contact and an interaction between the biomolecule placed on the biomolecule and a biomolecule sample applied from the sample applying section; 4) a detection section for detecting a signal caused by the biomolecule and a signal caused by the interaction, wherein the signal is an indicator for at least one information parameter of the organism, and the signal is related to an address assigned to the non-equal interval or the spot arrangement; and 5) a sending and receiving section for sending and receiving a signal, and B) a sub sub system, comprising: 1) a sending and receiving section for sending and receiving a signal; and 2) a test section for calculating a test value from the signal received from the main sub system, wherein the main sub system and the sub sub system are connected together via a network.
 80. A biological test system according to claim 79, wherein the signal received by the sub sub system contains a signal relating to measurement data measured by the sub sub system.
 81. A diagnosis system according to claim 79, wherein the attribute data contains chip ID, personal information data, and biomolecule attribute data, the main sub system contains the chip ID and the personal information data, but does not contain the biomolecule attribute data, and the sub sub system contains the chip ID and the biomolecule attribute data, but does not contain the personal information data, and the sub sub system sends the test value, determined in response to a request, to the main sub system.
 82. A diagnosis system according to claim 79, wherein the network is the Internet.
 83. A diagnosis system according to claim 79, wherein the signal to be sent and received is encrypted.
 84. A diagnosis system, comprising: A) a main sub system, comprising: 1) a biomolecule chip according to claim 27 or 30; 2) a sample applying section in fluid communication with the biomolecule chip; 3) a reaction control section for controlling a contact and an interaction between the biomolecule placed on the biomolecule and a biomolecule sample applied from the sample applying section; 4) a detection section for detecting a signal caused by the biomolecule and a signal caused by the interaction, wherein the signal is an indicator for at least one information parameter of the organism, and the signal is related to an address assigned to the non-equal interval or the spot arrangement; and 5) a sending and receiving section for sending and receiving a signal, and B) a sub sub system, comprising: 1) a sending and receiving section for sending and receiving a signal; and 2) a determination section for determining the diagnostic indicator from the signal received from the main sub system, wherein the main sub system and the sub sub system are connected together via a network.
 85. A diagnosis system according to claim 84, wherein the signal received by the sub sub system contains a signal relating to measurement data measured by the sub sub system.
 86. A diagnosis system according to claim 84, wherein the attribute data contains chip ID, personal information data, and biomolecule attribute data, the main sub system contains the chip ID and the personal information data, but does not contain the biomolecule attribute data, and the sub sub system contains the chip ID and the biomolecule attribute data, and data for determining a diagnostic indicator from biomolecule attribute data, but does not contain the personal information data, and the sub sub system sends the diagnostic indicator, determined in response to a request, to the main sub system.
 87. A diagnosis system according to claim 84, wherein the network is the Internet.
 88. A diagnosis system according to claim 84, wherein the signal to be sent and received is encrypted.
 89. A test apparatus for biological information, comprising: a support for a substrate; a plurality of groups of biomolecules arranged on the substrate, each group containining the biomolecules of the same type; shifting means for shifting the substrate; a light source for exciting a fluorescence substance labeling a sample to be tested; and optical means for converging light from the light source, wherein the light source is caused to emit light intermittently in response to an intermittent emission signal so as to excite the fluorescence substance, fluorescence from the fluorescence substance is detected by a photodetector during a period of time when the intermittent emission signal is paused, identification information is reproduced from an arrangement of the DNAs, and the biomolecules emitting fluorescence is identified.
 90. A test apparatus according to claim 89, further comprising means for adding up detected detection signals.
 91. A test apparatus according to claim 89, further comprising a wavelength separation mirror.
 92. Use of a biomolecule chip according to claim 12, 27, 30, 38, or 40 for fabricating an apparatus for testing biological information.
 93. Use of a biomolecule chip according to claim 12, 27, 30, 38, or 40 for fabricating an apparatus for diagnosing a subject. 